Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 61 of 120
Found at i:17404718 original size:40 final size:40
Alignment explanation
Indices: 17404641--17404811 Score: 193
Period size: 40 Copynumber: 4.3 Consensus size: 40
17404631 ATGCACATAC
* * * * *
17404641 GTACCCCTAAATGCTCATATGTGTCCTTGATTT-TACTTTG
1 GTACCCCTGAATGCACATACGTGCCCCTG-TTTGTACTTTG
* *
17404681 GTACCCCTGAATGTACATACGTG-CCTTAGTTTGTACTTTG
1 GTACCCCTGAATGCACATACGTGCCCCT-GTTTGTACTTTG
* *
17404721 GTACCCCTGAATGCACATACATGCCCCTATTTGTACTTTG
1 GTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTTG
* * *
17404761 GTGCCCCTGAATGCACTTACGTTCCCCTGTTTGTACTTTG
1 GTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTTG
*
17404801 GTACCTCTGAA
1 GTACCCCTGAA
17404812 AGCATTATAA
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
39 7 0.06
40 103 0.91
41 3 0.03
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (40 bp):
GTACCCCTGAATGCACATACGTGCCCCTGTTTGTACTTTG
Found at i:17406675 original size:25 final size:24
Alignment explanation
Indices: 17406647--17406719 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
17406637 GAGCTTTCTG
17406647 ATAATTGGCTCTTTGGAGCTTCCCA
1 ATAA-TGGCTCTTTGGAGCTTCCCA
*
17406672 ATAACTGGCTCTTAT-GAGCTTACCGA
1 ATAA-TGGCTCTT-TGGAGCTT-CCCA
* **
17406698 ATAATAGCTCTCCGGAGCTTCC
1 ATAATGGCTCTTTGGAGCTTCC
17406720 TGATATTGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 2 0.05
25 30 0.75
26 8 0.20
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (24 bp):
ATAATGGCTCTTTGGAGCTTCCCA
Found at i:17414370 original size:73 final size:73
Alignment explanation
Indices: 17414237--17414404 Score: 239
Period size: 73 Copynumber: 2.3 Consensus size: 73
17414227 AAGCTTGCAA
* * * * *
17414237 GAGCATCCCGTTATTAGCTC-TCATGAGCATCTCAATATTGGCTCTCTTGAGCTTCCTGATATAT
1 GAGCTTCCCGTTAATAGCTCTTC-GGATCATCTCAATATTGGCTCTCTTGAGCTTACTGATATAT
17414301 GGCACTCAC
65 GGCACTCAC
* * * *
17414310 GAGCTTTCTGTTAATAGCTCTTCGGATCATCTCGATATTGGCTCTCTTGAGCTTATTGATATATG
1 GAGCTTCCCGTTAATAGCTCTTCGGATCATCTCAATATTGGCTCTCTTGAGCTTACTGATATATG
17414375 GCACTCAC
66 GCACTCAC
17414383 GAGCTTCCCGTTAATAGCTCTT
1 GAGCTTCCCGTTAATAGCTCTT
17414405 TGGAGCATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
73 81 0.98
74 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (73 bp):
GAGCTTCCCGTTAATAGCTCTTCGGATCATCTCAATATTGGCTCTCTTGAGCTTACTGATATATG
GCACTCAC
Found at i:17414541 original size:25 final size:24
Alignment explanation
Indices: 17414456--17414592 Score: 82
Period size: 25 Copynumber: 5.5 Consensus size: 24
17414446 CATACCACAA
* * *
17414456 CTCTTACAAGCATCCTAATATTTGG
1 CTCTTACGAGCTTCCTAATA-ATGG
* *
17414481 CTCTTATGAGCTTCCCGTTAT-ATGG
1 CTCTTACGAGCTT-CC-TAATAATGG
* **
17414506 TTCTTGTGAGCTTCCTAATAATTGG
1 CTCTTACGAGCTTCCTAATAA-TGG
* **
17414531 CT-TTTCAGAGCTTCCCGATAACTGG
1 CTCTTAC-GAGCTTCCTAATAA-TGG
17414556 CTCTTACGAGCTTCCTGAATAATGG
1 CTCTTACGAGCTTCCT-AATAATGG
17414581 CTCTCTA-GAGCT
1 CTCT-TACGAGCT
17414593 AACTGATATT
Statistics
Matches: 87, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
23 3 0.03
24 5 0.06
25 65 0.75
26 11 0.13
27 3 0.03
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (24 bp):
CTCTTACGAGCTTCCTAATAATGG
Found at i:17414543 original size:50 final size:50
Alignment explanation
Indices: 17414456--17414592 Score: 138
Period size: 50 Copynumber: 2.7 Consensus size: 50
17414446 CATACCACAA
* * * *
17414456 CTCTTACAAGCATCCTAATATTTGGCTCTTATGAGCTTCCCGTTATA-TGG
1 CTCTTACGAGCTTCCTAATAATTGGCTCTTATGAGCTTCCCGATA-ACTGG
* ** *
17414506 TTCTTGTGAGCTTCCTAATAATTGGCTTTTCA-GAGCTTCCCGATAACTGG
1 CTCTTACGAGCTTCCTAATAATTGGCTCTT-ATGAGCTTCCCGATAACTGG
17414556 CTCTTACGAGCTTCCTGAATAA-TGGCTCTCTA-GAGCT
1 CTCTTACGAGCTTCCT-AATAATTGGCTCT-TATGAGCT
17414593 AACTGATATT
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
49 1 0.01
50 63 0.89
51 7 0.10
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (50 bp):
CTCTTACGAGCTTCCTAATAATTGGCTCTTATGAGCTTCCCGATAACTGG
Found at i:17414598 original size:25 final size:24
Alignment explanation
Indices: 17414547--17414607 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
17414537 AGAGCTTCCC
**
17414547 GATAACTGGCTCTTACGAGCTTCCT
1 GATAA-TGGCTCTTACGAGCTAACT
17414572 GAATAATGGCTCTCTA-GAGCTAACT
1 G-ATAATGGCTCT-TACGAGCTAACT
*
17414597 GATATTGGCTC
1 GATAATGGCTC
17414608 GCATGAACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 9 0.29
25 16 0.52
26 6 0.19
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (24 bp):
GATAATGGCTCTTACGAGCTAACT
Found at i:17420131 original size:27 final size:27
Alignment explanation
Indices: 17420041--17420160 Score: 82
Period size: 27 Copynumber: 4.5 Consensus size: 27
17420031 GTAGTCTTTT
* * *
17420041 GGGACACTAAAC-AGTGGTAGCCCGTC
1 GGGACACTAAACAAGGGGTAGTCCGCC
* * * * *
17420067 AGAACACTAAACACGGGGTACTCCGCT
1 GGGACACTAAACAAGGGGTAGTCCGCC
* * * * *
17420094 TGAACAATAAACATGGGGTAGT-CGATC
1 GGGACACTAAACAAGGGGTAGTCCG-CC
* *
17420121 GGGATACTAAACAAGTGGTAGTCCGCC
1 GGGACACTAAACAAGGGGTAGTCCGCC
17420148 GGGACACTAAACA
1 GGGACACTAAACA
17420161 CAATAATCCA
Statistics
Matches: 69, Mismatches: 22, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
26 12 0.17
27 55 0.80
28 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (27 bp):
GGGACACTAAACAAGGGGTAGTCCGCC
Found at i:17422667 original size:33 final size:33
Alignment explanation
Indices: 17422625--17422777 Score: 113
Period size: 33 Copynumber: 4.5 Consensus size: 33
17422615 TTCCCTGAGG
17422625 GGTTGCTAAGTGCTGATTCCCCTAATT-ATTGGT
1 GGTTGCTAAGTGCTGATTCCCCT-ATTAATTGGT
* *
17422658 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-AAT-T----GGT
**
17422701 GGTTGCTAAGTGCTGATTCCCC---CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
*
17422728 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
17422761 GGTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
17422778 CCCACCGCAT
Statistics
Matches: 96, Mismatches: 7, Indels: 34
0.70 0.05 0.25
Matches are distributed among these distances:
27 22 0.23
28 2 0.02
30 1 0.01
32 2 0.02
33 36 0.38
34 3 0.03
35 2 0.02
36 2 0.02
38 2 0.02
39 1 0.01
42 2 0.02
43 21 0.22
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
Found at i:17422696 original size:102 final size:104
Alignment explanation
Indices: 17422519--17422886 Score: 577
Period size: 102 Copynumber: 3.6 Consensus size: 104
17422509 TTGCATATAA
** *
17422519 AGGGGTTGCTGTGTGCTGATTCCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
1 AGGGGTTGCTAAGTGCTGATTCCCCTGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
*
17422584 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATT-CCCTG
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
*
17422622 AGGGGTTGCTAAGTGCTGATTCCCCTAATT-ATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
1 AGGGGTTGCTAAGTGCTGATTCCCCTGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
17422686 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
* *
17422725 AGGGGTTGCTAAGTGCTGATTCCCCT-ATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGCATC
1 AGGGGTTGCTAAGTGCTGATTCCCCTGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
* *
17422789 TGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCCA
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
** *
17422827 AGGGGTTGCTGCGTGCTGATTCCCC-GATTCATTGGTGGTTGCTAGGTGCTGAAT-CCACCG
1 AGGGGTTGCTAAGTGCTGATTCCCCTGATTCATTGGTGGTTGCTAAGTGCTG-ATCCCACCG
17422887 ATAACGGTTA
Statistics
Matches: 249, Mismatches: 12, Indels: 9
0.92 0.04 0.03
Matches are distributed among these distances:
102 151 0.61
103 98 0.39
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCTGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:17430185 original size:76 final size:76
Alignment explanation
Indices: 17430105--17430280 Score: 300
Period size: 76 Copynumber: 2.3 Consensus size: 76
17430095 TGCATATAAA
** * *
17430105 GGGGTTGCTGTGTGCTAATTCCCC-GATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTT
1 GGGGTTGCTAAGTGCTGATTCCCCTAATT-ATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTT
17430169 TAAATGTGAAAG
65 TAAATGTGAAAG
17430181 GGGGTTGCTAAGTGCTGATTCCCCTAATTATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCTAATTATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTT
17430246 AAATGTGAAAG
66 AAATGTGAAAG
17430257 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
17430281 CGAGGGGTTG
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
76 92 0.97
77 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.34
Consensus pattern (76 bp):
GGGGTTGCTAAGTGCTGATTCCCCTAATTATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTT
AAATGTGAAAG
Found at i:17430188 original size:43 final size:43
Alignment explanation
Indices: 17430140--17430275 Score: 175
Period size: 43 Copynumber: 3.4 Consensus size: 43
17430130 ATTCATTGGT
17430140 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
* * *
17430183 GGTTGCTAAGTGCTGATTCC-CC-TA-ATT--AT-T----GGT
1 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
17430216 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
17430259 GGTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
17430276 TCCCCCGAGG
Statistics
Matches: 77, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
33 21 0.27
34 2 0.03
35 2 0.03
36 2 0.03
37 1 0.01
38 4 0.05
39 1 0.01
40 2 0.03
41 2 0.03
42 2 0.03
43 38 0.49
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
Found at i:17430225 original size:33 final size:33
Alignment explanation
Indices: 17430183--17430335 Score: 113
Period size: 33 Copynumber: 4.5 Consensus size: 33
17430173 TGTGAAAGGG
17430183 GGTTGCTAAGTGCTGATTCCCCTAATT-ATTGGT
1 GGTTGCTAAGTGCTGATTCCCCT-ATTAATTGGT
* *
17430216 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-AAT-T----GGT
**
17430259 GGTTGCTAAGTGCTGATTCCCC---CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
*
17430286 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
17430319 GGTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
17430336 CCCACCGCAT
Statistics
Matches: 96, Mismatches: 7, Indels: 34
0.70 0.05 0.25
Matches are distributed among these distances:
27 22 0.23
28 2 0.02
30 1 0.01
32 2 0.02
33 36 0.38
34 3 0.03
35 2 0.02
36 2 0.02
38 2 0.02
39 1 0.01
42 2 0.02
43 21 0.22
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCTATTAATTGGT
Found at i:17430300 original size:103 final size:103
Alignment explanation
Indices: 17430181--17430445 Score: 410
Period size: 103 Copynumber: 2.6 Consensus size: 103
17430171 AATGTGAAAG
* *
17430181 GGGGTTGCTAAGTGCTGATTCCCCTAATT-ATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTT
1 GGGGTTGCTAAGTGCTGATTCCCCT-ATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGCATCT
* *
17430245 TAAATGTGAAAGGGGGTTGCTAAGTGCTGATT-CCCCCGA
65 GAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCCCAA
17430284 GGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGCATCTG
1 GGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGCATCTG
17430349 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCCAA
66 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCCAA
*** *
17430387 GGGGTTGCTGTTTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGAAT-CCACCG
1 GGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTG-ATCCCACCG
17430446 ATAACGGTTA
Statistics
Matches: 151, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
102 26 0.17
103 123 0.81
104 2 0.01
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (103 bp):
GGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGCATCTG
AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCCAA
Found at i:17437066 original size:2 final size:2
Alignment explanation
Indices: 17437059--17437094 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17437049 TGTGTATTAG
17437059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17437095 CATGGATGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17438218 original size:54 final size:54
Alignment explanation
Indices: 17438160--17438262 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
17438150 GTGTAATTTT
* * *
17438160 CACACGGCCTAAGACACGGCCGTGTGTCTCAAGTTAGTGAGATACACGGCATAG
1 CACACAGCCTAAGACACGGCCGTGTGTCACAACTTAGTGAGATACACGGCATAG
** * * *
17438214 CACACAGCCTGCGAGACGGCTGTGTGTCACAACTTAGTGAGTTACACGG
1 CACACAGCCTAAGACACGGCCGTGTGTCACAACTTAGTGAGATACACGG
17438263 TTTAAGACAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (54 bp):
CACACAGCCTAAGACACGGCCGTGTGTCACAACTTAGTGAGATACACGGCATAG
Found at i:17453528 original size:18 final size:17
Alignment explanation
Indices: 17453501--17453535 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17453491 TAACTTGTCC
17453501 ATTATGTAGCCCACAATG
1 ATTATGTAGCCCA-AATG
*
17453519 ATTATTTAGCCCAAATG
1 ATTATGTAGCCCAAATG
17453536 GCTGGCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (17 bp):
ATTATGTAGCCCAAATG
Found at i:17468735 original size:15 final size:15
Alignment explanation
Indices: 17468715--17468751 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
17468705 GGCTTTCCAA
17468715 CTGATTGCACAACCT
1 CTGATTGCACAACCT
17468730 CTGATTGCACAACCT
1 CTGATTGCACAACCT
17468745 CTGATTG
1 CTGATTG
17468752 TAAAGACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (15 bp):
CTGATTGCACAACCT
Found at i:17470322 original size:49 final size:49
Alignment explanation
Indices: 17470195--17470371 Score: 203
Period size: 49 Copynumber: 3.6 Consensus size: 49
17470185 GGGCTTGAAA
* * * * *
17470195 ATATCTTATGTTCCTCAACCATTCTGATAAGCGTGTTAGGTTTGAGAGC
1 ATATCTTATGTTCCTCAGCCATTCTGATAAGTGTGTTAAGTGTGAGAAC
* * * *
17470244 ATACCTTATGTACCT-AGCCATTTTGATAAGTGTGTTAAGTGTGGGAAC
1 ATATCTTATGTTCCTCAGCCATTCTGATAAGTGTGTTAAGTGTGAGAAC
* * * *
17470292 ATATTTTATGTTTCTCAGCCATTCTAATAAGTGCGTTAAGTGTGAGAAC
1 ATATCTTATGTTCCTCAGCCATTCTGATAAGTGTGTTAAGTGTGAGAAC
* * *
17470341 ATATTTTATGTTTCTCAGCCATTTTGATAAG
1 ATATCTTATGTTCCTCAGCCATTCTGATAAG
17470372 ATAAGTATTT
Statistics
Matches: 108, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
48 37 0.34
49 71 0.66
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (49 bp):
ATATCTTATGTTCCTCAGCCATTCTGATAAGTGTGTTAAGTGTGAGAAC
Found at i:17470350 original size:97 final size:98
Alignment explanation
Indices: 17470195--17470371 Score: 230
Period size: 97 Copynumber: 1.8 Consensus size: 98
17470185 GGGCTTGAAA
* * * * *
17470195 ATATCTTATGTTCCTCAACCATTCTGATAAGCGTGTTAGGTTTGAGAGCATACCTTATGTACCT-
1 ATATCTTATGTTCCTCAACCATTCTAATAAGCGCGTTAAGTGTGAGAACATACCTTATGTACCTC
17470259 AGCCATTTTGATAAGTGTGTTAAGTGTGGGAAC
66 AGCCATTTTGATAAGTGTGTTAAGTGTGGGAAC
* * * * ** **
17470292 ATATTTTATGTTTCTCAGCCATTCTAATAAGTGCGTTAAGTGTGAGAACATATTTTATGTTTCTC
1 ATATCTTATGTTCCTCAACCATTCTAATAAGCGCGTTAAGTGTGAGAACATACCTTATGTACCTC
17470357 AGCCATTTTGATAAG
66 AGCCATTTTGATAAG
17470372 ATAAGTATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
97 51 0.77
98 15 0.23
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (98 bp):
ATATCTTATGTTCCTCAACCATTCTAATAAGCGCGTTAAGTGTGAGAACATACCTTATGTACCTC
AGCCATTTTGATAAGTGTGTTAAGTGTGGGAAC
Found at i:17481956 original size:14 final size:14
Alignment explanation
Indices: 17481921--17481957 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17481911 TTATTTGATG
17481921 TGGTAAATGTTGCA
1 TGGTAAATGTTGCA
*
17481935 TGGCAAATGTTGCA
1 TGGTAAATGTTGCA
*
17481949 TGTTAAATG
1 TGGTAAATG
17481958 GATTTCAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (14 bp):
TGGTAAATGTTGCA
Found at i:17483660 original size:18 final size:20
Alignment explanation
Indices: 17483637--17483679 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 20
17483627 ACATCACACA
17483637 ACTTTTG-TAACAC-GTT-TC
1 ACTTTTGCTAA-ACTGTTGTC
17483655 ACTTTTGCTAAACTGTTGTC
1 ACTTTTGCTAAACTGTTGTC
17483675 ACTTT
1 ACTTT
17483680 CTCCCTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.41
19 6 0.27
20 7 0.32
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (20 bp):
ACTTTTGCTAAACTGTTGTC
Found at i:17485470 original size:14 final size:15
Alignment explanation
Indices: 17485430--17485485 Score: 80
Period size: 14 Copynumber: 3.8 Consensus size: 15
17485420 AGAGTTGAGA
*
17485430 GAGAGGATGATAGAT
1 GAGAGGATGATGGAT
17485445 GAGAGGGATGATGGAT
1 GAGA-GGATGATGGAT
17485461 GAGA-GATGATGGAT
1 GAGAGGATGATGGAT
17485475 GAG-GGATGATG
1 GAGAGGATGATG
17485486 AATAAAGTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
14 20 0.53
15 4 0.11
16 14 0.37
ACGTcount: A:0.34, C:0.00, G:0.46, T:0.20
Consensus pattern (15 bp):
GAGAGGATGATGGAT
Found at i:17486944 original size:286 final size:286
Alignment explanation
Indices: 17486432--17487002 Score: 1088
Period size: 286 Copynumber: 2.0 Consensus size: 286
17486422 TTTTATGGCA
17486432 CAAAAGAGCTTGTGGTCCAGTGTCAAGATGGCGTGGGGTGTAACTATAAGGTCTGAGGTTCAAGT
1 CAAAAGAGCTTGTGGTCCAGTGTCAAGATGGCGTGGGGTGTAACTATAAGGTCTGAGGTTCAAGT
*
17486497 CCTAGGTTGTGCATTGGAGTATTGATCTTGCTGCTGGAGCTGTGTAGGTAGTGGAGTTGAATTGA
66 CCTAGGTTCTGCATTGGAGTATTGATCTTGCTGCTGGAGCTGTGTAGGTAGTGGAGTTGAATTGA
17486562 AACACAGCTAAGGAGTGTTTGAATGGAATTTGAATGGAGTTGTTGGGGGAGTTAATAAGAAATTG
131 AACACAGCTAAGGAGTGTTTGAATGGAATTTGAATGGAGTTGTTGGGGGAGTTAATAAGAAATTG
17486627 GTGGAGTGATTCAAGGAGAGTGATTTTAGGAGAAAATTAAGGGAAGTGAGGGAGAGGGGAGTGGT
196 GTGGAGTGATTCAAGGAGAGTGATTTTAGGAGAAAATTAAGGGAAGTGAGGGAGAGGGGAGTGGT
17486692 GCCAAAAATGGACTTGTTACGCAGAC
261 GCCAAAAATGGACTTGTTACGCAGAC
*
17486718 CAAAAGAGCTTGTGGTCCAGTGTCAAGGTGGCGTGGGGTGTAACTATAAGGTCTGAGGTTCAAGT
1 CAAAAGAGCTTGTGGTCCAGTGTCAAGATGGCGTGGGGTGTAACTATAAGGTCTGAGGTTCAAGT
*
17486783 CCTAGGTTCTGCATTGGAGTATTTATCTTGCTGCTGGAGCTGTGTAGGTAGTGGAGTTGAATTGA
66 CCTAGGTTCTGCATTGGAGTATTGATCTTGCTGCTGGAGCTGTGTAGGTAGTGGAGTTGAATTGA
* *
17486848 AACACAGCTAAGGAGTGTTTGAATGGAATTTGAATGGATTTGTTGGGGGAGTTAATAATAAATTG
131 AACACAGCTAAGGAGTGTTTGAATGGAATTTGAATGGAGTTGTTGGGGGAGTTAATAAGAAATTG
17486913 GTGGAGTGATTCAAGGAGAGTGATTTTAGGAGAAAATTAAGGGAAGTGAGGGAGAGGGGAGTGGT
196 GTGGAGTGATTCAAGGAGAGTGATTTTAGGAGAAAATTAAGGGAAGTGAGGGAGAGGGGAGTGGT
*
17486978 GCCGAAAATGGACTTGTTACGCAGA
261 GCCAAAAATGGACTTGTTACGCAGA
17487003 AAAATTCGAC
Statistics
Matches: 279, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
286 279 1.00
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (286 bp):
CAAAAGAGCTTGTGGTCCAGTGTCAAGATGGCGTGGGGTGTAACTATAAGGTCTGAGGTTCAAGT
CCTAGGTTCTGCATTGGAGTATTGATCTTGCTGCTGGAGCTGTGTAGGTAGTGGAGTTGAATTGA
AACACAGCTAAGGAGTGTTTGAATGGAATTTGAATGGAGTTGTTGGGGGAGTTAATAAGAAATTG
GTGGAGTGATTCAAGGAGAGTGATTTTAGGAGAAAATTAAGGGAAGTGAGGGAGAGGGGAGTGGT
GCCAAAAATGGACTTGTTACGCAGAC
Found at i:17487907 original size:27 final size:26
Alignment explanation
Indices: 17487868--17488348 Score: 404
Period size: 27 Copynumber: 17.9 Consensus size: 26
17487858 GTTATGACGA
*
17487868 AAATACCCCCATAGGGTAAAATAACCG
1 AAATA-CCCCATAGGGTAAAATGACCG
17487895 AAATACCCGCATAGGGTAAAATGACCG
1 AAATACCC-CATAGGGTAAAATGACCG
*
17487922 AAATACCCCCATAAGGTAAAATGACCG
1 AAATA-CCCCATAGGGTAAAATGACCG
* * *
17487949 AAATACCCCATAGGGTAACATAACAG
1 AAATACCCCATAGGGTAAAATGACCG
* *
17487975 ACATACCCCAATTGGGTAAAA-GACCG
1 AAATACCCC-ATAGGGTAAAATGACCG
* * * *
17488001 AAATATACCCATAGAGTAAAATTAACG
1 AAATA-CCCCATAGGGTAAAATGACCG
* *
17488028 AAATACCCTTATTGGGTAAAATGACCG
1 AAATACCC-CATAGGGTAAAATGACCG
* * *
17488055 AAATACCCTTATAGGGTAAAATAACTG
1 AAATACCC-CATAGGGTAAAATGACCG
*
17488082 AAATACCCTCATAGGGTAAAATGACCA
1 AAATACCC-CATAGGGTAAAATGACCG
**
17488109 AAATAACCCCATAGGGTAAAATGACTA
1 AAAT-ACCCCATAGGGTAAAATGACCG
*
17488136 AAATACCCCCATAGGGTAAAATGACTG
1 AAATA-CCCCATAGGGTAAAATGACCG
*
17488163 AAATACCCTCGA-AAGGTAAAATGACCG
1 AAATACCC-C-ATAGGGTAAAATGACCG
17488190 AAATACCCC-TGAAGGGTAAAATGACC-
1 AAATACCCCAT--AGGGTAAAATGACCG
* *
17488216 ATAATAACCTCGA-AGGGTAAAATGACCA
1 A-AAT-ACC-CCATAGGGTAAAATGACCG
* *
17488244 AAATGCCCCCGA-AGGGTGAAATGACC-
1 AAAT-ACCCC-ATAGGGTAAAATGACCG
* * *
17488270 AGAATACCCC-TGAAGGGTGAAATGATCA
1 A-AATACCCCAT--AGGGTAAAATGACCG
* *
17488298 AAATACCCCCGA-AGGGTCAAATGATCG
1 AAATA-CCCC-ATAGGGTAAAATGACCG
*
17488325 AAATACCCCCTAGGGTAAAATGAC
1 AAATACCCCATAGGGTAAAATGAC
17488349 TGTTATACCC
Statistics
Matches: 379, Mismatches: 47, Indels: 57
0.78 0.10 0.12
Matches are distributed among these distances:
26 73 0.19
27 288 0.76
28 17 0.04
29 1 0.00
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (26 bp):
AAATACCCCATAGGGTAAAATGACCG
Found at i:17487926 original size:54 final size:53
Alignment explanation
Indices: 17487868--17488348 Score: 449
Period size: 54 Copynumber: 9.0 Consensus size: 53
17487858 GTTATGACGA
*
17487868 AAATACCCCCATAGGGTAAAATAACCGAAATACCCGCATAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCGAAATACCC-CATAGGGTAAAATGACCG
* * * *
17487922 AAATACCCCCATAAGGTAAAATGACCGAAATACCCCATAGGGTAACATAACAG
1 AAATACCCCCATAGGGTAAAATGACCGAAATACCCCATAGGGTAAAATGACCG
* * * * * * *
17487975 ACATACCCCAATTGGGTAAAA-GACCGAAATATACCCATAGAGTAAAATTAACG
1 AAATACCCCCATAGGGTAAAATGACCGAAATA-CCCCATAGGGTAAAATGACCG
** * * * *
17488028 AAATACCCTTATTGGGTAAAATGACCGAAATACCCTTATAGGGTAAAATAACTG
1 AAATACCCCCATAGGGTAAAATGACCGAAATACCC-CATAGGGTAAAATGACCG
* * **
17488082 AAATACCCTCATAGGGTAAAATGACCAAAATAACCCCATAGGGTAAAATGACTA
1 AAATACCCCCATAGGGTAAAATGACCGAAAT-ACCCCATAGGGTAAAATGACCG
* *
17488136 AAATACCCCCATAGGGTAAAATGACTGAAATACCCTCGA-AAGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCGAAATACCC-C-ATAGGGTAAAATGACCG
* * *
17488190 AAATACCCCTGA-AGGGTAAAATGACC-ATAATAACCTCGA-AGGGTAAAATGACCA
1 AAATACCCC-CATAGGGTAAAATGACCGA-AAT-ACC-CCATAGGGTAAAATGACCG
* * * * *
17488244 AAATGCCCCCGA-AGGGTGAAATGACC-AGAATACCCC-TGAAGGGTGAAATGATCA
1 AAATACCCCC-ATAGGGTAAAATGACCGA-AATACCCCAT--AGGGTAAAATGACCG
* * *
17488298 AAATACCCCCGA-AGGGTCAAATGATCGAAATACCCCCTAGGGTAAAATGAC
1 AAATACCCCC-ATAGGGTAAAATGACCGAAATACCCCATAGGGTAAAATGAC
17488349 TGTTATACCC
Statistics
Matches: 358, Mismatches: 53, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
52 11 0.03
53 86 0.24
54 249 0.70
55 11 0.03
56 1 0.00
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (53 bp):
AAATACCCCCATAGGGTAAAATGACCGAAATACCCCATAGGGTAAAATGACCG
Found at i:17488549 original size:26 final size:26
Alignment explanation
Indices: 17488510--17488564 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
17488500 TGGAGGAAGT
*
17488510 ATACTATTATTGGCAGCTTTGCGGCG
1 ATACTATTACTGGCAGCTTTGCGGCG
* *
17488536 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCGGCG
17488562 ATA
1 ATA
17488565 TTAGTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCGGCG
Found at i:17488718 original size:28 final size:28
Alignment explanation
Indices: 17488681--17488798 Score: 168
Period size: 28 Copynumber: 4.3 Consensus size: 28
17488671 CACTGTACTG
17488681 GTTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
17488709 GTTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* *
17488737 ATTACTGTATTGGGCTAAGGCCTACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* * * *
17488765 ATTATTTTATTGGGCTAATG-CCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
17488792 G-TACTGT
1 GTTACTGT
17488799 TACTAAATAG
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 4 0.05
27 6 0.07
28 71 0.88
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:17500747 original size:320 final size:307
Alignment explanation
Indices: 17500099--17500760 Score: 858
Period size: 320 Copynumber: 2.1 Consensus size: 307
17500089 CCATATTCAT
* *
17500099 TGAACTCAACAGGAAAATTCTTTTTGTCTACTAATGTGGTGATGAAACTACATTTGTAATACAAT
1 TGAACTCAACAGGAAAATTCTTTTTGTCTACTAATATGGTGATGAAACTACATTTGTAATAAAAT
* * * * *
17500164 CGGCCCCATCTACCCTAACACAAATAAATTCACCATTCAGACATTTGAAATTAACTTGTTTCCTT
66 CAGCCCCATCTACCCTAACACAAATAAATTCACCATCCAAACATTTCAAACTAACTTGTTTCCTT
* **
17500229 CGGCAACAACATCAAACCAGTGGGAACCAATCAATGTCCAGAATAAGATCAAAATCATCAAAAGG
131 CGACAACAACATCAAACCAGTAAGAACCAATCAATGTCCAGAATAAGATCAAAATCATCAAAAGG
* ** *
17500294 ATCAAACCAGTGGGAAAATCGTAACCCCTAACTTTTAGTGGACACAATTTACATATTTGATTAAC
196 ATCAAACCAGCGAAAAAATCGTAACCCCTAACTTTTAGTGGACACAATGTACATATTTGATTAAC
* *
17500359 TAAAACACACTGACCTAGTGGATTTGTTACTTTGAAAGTATATTCAA
261 TAAAACACACTGACCCAGTGGATTTGTTACTTTGAAAGTATACTCAA
*
17500406 TGAACTCAACAGGAAAATTCTTTTTGTCTACTAATATGGTGCTGAAACTACATTTGTAATAAAAT
1 TGAACTCAACAGGAAAATTCTTTTTGTCTACTAATATGGTGATGAAACTACATTTGTAATAAAAT
* * *
17500471 CAGCCCCATTTGCCCTAACACAAATAAATTCACCATCCAAACGTTTCAAACTAACTTGTTTCCTT
66 CAGCCCCATCTACCCTAACACAAATAAATTCACCATCCAAACATTTCAAACTAACTTGTTTCCTT
* * *** * * * *
17500536 TGACAACTCACTATTGCATCATGCTCAAATAACCAATCCATTTCCAGAATAAGATCAAAATCATC
131 CGACAAC-AAC-ATCAAACCA-G-T--AAGAACCAATCAATGTCCAGAATAAGATCAAAATCATC
* * *
17500601 GAAAGGTAACAACATCAAACTAGCGAAAAAATCGTCACCCCTAACTTTTAGTGGACACAATGTAC
190 AAAAGG-------ATCAAACCAGCGAAAAAATCGTAACCCCTAACTTTTAGTGGACACAATGTAC
* * *
17500666 ATATCTT-ATTCACTAAAACACACTGACCCAGTGGATTTGTTACTTTGACAGTATACTCAG
248 ATAT-TTGATTAACTAAAACACACTGACCCAGTGGATTTGTTACTTTGAAAGTATACTCAA
* *
17500726 TGAACTTAACAGGAAAATTCTTTTTATCTACTAAT
1 TGAACTCAACAGGAAAATTCTTTTTGTCTACTAAT
17500761 GTGATGCATA
Statistics
Matches: 304, Mismatches: 37, Indels: 15
0.85 0.10 0.04
Matches are distributed among these distances:
307 124 0.41
308 2 0.01
309 5 0.02
310 1 0.00
311 1 0.00
313 38 0.12
320 131 0.43
321 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (307 bp):
TGAACTCAACAGGAAAATTCTTTTTGTCTACTAATATGGTGATGAAACTACATTTGTAATAAAAT
CAGCCCCATCTACCCTAACACAAATAAATTCACCATCCAAACATTTCAAACTAACTTGTTTCCTT
CGACAACAACATCAAACCAGTAAGAACCAATCAATGTCCAGAATAAGATCAAAATCATCAAAAGG
ATCAAACCAGCGAAAAAATCGTAACCCCTAACTTTTAGTGGACACAATGTACATATTTGATTAAC
TAAAACACACTGACCCAGTGGATTTGTTACTTTGAAAGTATACTCAA
Found at i:17502649 original size:54 final size:54
Alignment explanation
Indices: 17502591--17502735 Score: 195
Period size: 54 Copynumber: 2.7 Consensus size: 54
17502581 TCCTAGCCCG
* *
17502591 TGTGCTAGGTCGTGTAACTCAT-TGAATTGCC-CTACACGCCCGTGTACCAGGTCA
1 TGTGCTAGGTCGTGTAACTC-TCTGAATTGCCAC-ACACGACCGTGTACCAGGCCA
* *
17502645 TGTGCTAGGTCGTGTAACTCTCTGAGTTGCCACACACGACCGTGTGCCAGGCCA
1 TGTGCTAGGTCGTGTAACTCTCTGAATTGCCACACACGACCGTGTACCAGGCCA
* * *
17502699 TGTGTTAGGACGTGTAACTCTCTGAGTTGCCACACAC
1 TGTGCTAGGTCGTGTAACTCTCTGAATTGCCACACAC
17502736 TCTCATGTGC
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
53 1 0.01
54 81 0.98
55 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.27
Consensus pattern (54 bp):
TGTGCTAGGTCGTGTAACTCTCTGAATTGCCACACACGACCGTGTACCAGGCCA
Found at i:17502745 original size:54 final size:54
Alignment explanation
Indices: 17502591--17502772 Score: 190
Period size: 54 Copynumber: 3.4 Consensus size: 54
17502581 TCCTAGCCCG
* * * * * * *
17502591 TGTGCTAGGTCGTGTAACTCAT-TGAATTGCC-CTACACGCCCGTGTACCAGGTCA
1 TGTGTTAGGACGTGTAACTC-TCTGAGTTGCCAC-ACACGACCATGTGCCAGGCCA
* * *
17502645 TGTGCTAGGTCGTGTAACTCTCTGAGTTGCCACACACGACCGTGTGCCAGGCCA
1 TGTGTTAGGACGTGTAACTCTCTGAGTTGCCACACACGACCATGTGCCAGGCCA
*
17502699 TGTGTTAGGACGTGTAACTCTCTGAGTTGCCACACAC-TCTCATGTGCCAGGCCA
1 TGTGTTAGGACGTGTAACTCTCTGAGTTGCCACACACGAC-CATGTGCCAGGCCA
* * *
17502753 TGAGTTCGGATGTGTAACTC
1 TGTGTTAGGACGTGTAACTC
17502773 ATTGACTTGA
Statistics
Matches: 114, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
53 2 0.02
54 111 0.97
55 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (54 bp):
TGTGTTAGGACGTGTAACTCTCTGAGTTGCCACACACGACCATGTGCCAGGCCA
Found at i:17505052 original size:21 final size:21
Alignment explanation
Indices: 17505028--17505070 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17505018 TTTTTAATAA
17505028 GACTAAGTCCTAGGGAGATTT
1 GACTAAGTCCTAGGGAGATTT
17505049 GACTAAGTCCTAGGGAGATTT
1 GACTAAGTCCTAGGGAGATTT
17505070 G
1 G
17505071 TTAGCTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (21 bp):
GACTAAGTCCTAGGGAGATTT
Found at i:17512568 original size:40 final size:39
Alignment explanation
Indices: 17512502--17512600 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 39
17512492 TCTCATTATA
17512502 AATATTTTATTGTTAATAAAAATTTAATATAAAAATTC-
1 AATATTTTATTGTTAATAAAAATTTAATATAAAAATTCG
* *
17512540 AATATTTTATT-TTAATAATATTTATTTAATATAAAATTTCG
1 AATATTTTATTGTTAATAA-A--AATTTAATATAAAAATTCG
17512581 ATATATTTTATTGTTAATAA
1 A-ATATTTTATTGTTAATAA
17512601 CATTATATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
37 7 0.13
38 12 0.23
40 16 0.30
41 1 0.02
42 10 0.19
43 7 0.13
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (39 bp):
AATATTTTATTGTTAATAAAAATTTAATATAAAAATTCG
Found at i:17520308 original size:21 final size:21
Alignment explanation
Indices: 17520257--17520308 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
17520247 TTATATTAGT
* *
17520257 TTTTATTTATTTATTTACTTA
1 TTTTATTTTTTTATTGACTTA
* *
17520278 TTATTA-TTTTTTATTGGCTTG
1 TT-TTATTTTTTTATTGACTTA
17520299 TTTTATTTTT
1 TTTTATTTTT
17520309 ATTTTCGCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTATTTTTTTATTGACTTA
Found at i:17520379 original size:3 final size:3
Alignment explanation
Indices: 17520371--17520424 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
17520361 CAAAACTTAG
*
17520371 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
17520419 GTT ATT
1 ATT ATT
17520425 TATATTGTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:17524577 original size:18 final size:18
Alignment explanation
Indices: 17524556--17524618 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
17524546 ACAGTTTGAA
17524556 ATATTAATACAGTTCGCC
1 ATATTAATACAGTTCGCC
* * *
17524574 ATATTAATATAGATCACC
1 ATATTAATACAGTTCGCC
* * *
17524592 AAATTAACACAGTTCGAC
1 ATATTAATACAGTTCGCC
*
17524610 ATAATAATA
1 ATATTAATA
17524619 TAATTCACCA
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.30
Consensus pattern (18 bp):
ATATTAATACAGTTCGCC
Found at i:17524604 original size:36 final size:36
Alignment explanation
Indices: 17524558--17524636 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
17524548 AGTTTGAAAT
* * *
17524558 ATTAATACAGTTCGCCATATTAATATAGA-TCACCAA
1 ATTAACACAGTTCGACATAATAATATA-ATTCACCAA
17524594 ATTAACACAGTTCGACATAATAATATAATTCACCAA
1 ATTAACACAGTTCGACATAATAATATAATTCACCAA
*
17524630 GTTAACA
1 ATTAACA
17524637 TGGTTCACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 1 0.03
36 37 0.97
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (36 bp):
ATTAACACAGTTCGACATAATAATATAATTCACCAA
Found at i:17525599 original size:133 final size:133
Alignment explanation
Indices: 17525361--17525625 Score: 494
Period size: 133 Copynumber: 2.0 Consensus size: 133
17525351 ATACACATCA
*
17525361 AACACCTTACAAAGGCATTACGAACATCAACAAACACCATTAAATAATTTGCAAATCATAAATCA
1 AACACCTTACAAAGGCATTACGAACATCAACAAACACCATTAAATAATTTCCAAATCATAAATCA
17525426 AAGCCTATTAACCTCTATACCGAAAATTTAACTAGTTTTATCGAAATATGTGTTTAACCACTCAA
66 AAGCCTATTAACCTCTATACCGAAAATTTAACTAGTTTTATCGAAATATGTGTTTAACCACTCAA
17525491 ATT
131 ATT
* *
17525494 AACACTTTACAAAGGCATTACGAACATCAACAAACACCATTAAATCATTTCCAAATCATAAATCA
1 AACACCTTACAAAGGCATTACGAACATCAACAAACACCATTAAATAATTTCCAAATCATAAATCA
*
17525559 AAGCCTATTAACCTCTATACCGAACATTTAACTAGTTTTATCGAAATATGTGTTTAACCACTCAA
66 AAGCCTATTAACCTCTATACCGAAAATTTAACTAGTTTTATCGAAATATGTGTTTAACCACTCAA
17525624 AT
131 AT
17525626 ATCACTTCTA
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 128 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (133 bp):
AACACCTTACAAAGGCATTACGAACATCAACAAACACCATTAAATAATTTCCAAATCATAAATCA
AAGCCTATTAACCTCTATACCGAAAATTTAACTAGTTTTATCGAAATATGTGTTTAACCACTCAA
ATT
Found at i:17526483 original size:23 final size:21
Alignment explanation
Indices: 17526447--17526490 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
17526437 ATTTTAATAT
17526447 TTTAATTAATTAATTCCTAATTA
1 TTTAATTAATTAA-T-CTAATTA
17526470 TTTAATT-ATATAATCTAATTA
1 TTTAATTAAT-TAATCTAATTA
17526491 CGGTTTTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAATTAATTAATCTAATTA
Found at i:17526489 original size:32 final size:31
Alignment explanation
Indices: 17526420--17526490 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
17526410 CTTAACCTAA
*
17526420 AATT-ATTAATTCTAATTATTTTAATATTTT
1 AATTAATTAATTCTAATTATTTTAATATTAT
17526450 AATTAATTAATTCCTAATTA-TTTAAT-TATAT
1 AATTAATTAATT-CTAATTATTTTAATAT-TAT
17526481 AATCTAATTA
1 AAT-TAATTA
17526491 CGGTTTTCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 5 0.14
31 18 0.50
32 13 0.36
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (31 bp):
AATTAATTAATTCTAATTATTTTAATATTAT
Found at i:17533836 original size:51 final size:50
Alignment explanation
Indices: 17533709--17533842 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 50
17533699 AAAGTGATGG
* * *
17533709 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATAATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAAATAATAGA
* * * * * *
17533759 TCGCATGTGTAGTACTATGTGCAGGCTATTATGCGTACC-AAATAGTTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAAATA--ATAGA
17533810 TCACGTGTGTAGTACTATGTGCAGGCTACTACG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACG
17533843 TGTATCGGAT
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
49 4 0.06
50 34 0.49
51 31 0.45
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAAATAATAGA
Found at i:17533874 original size:51 final size:51
Alignment explanation
Indices: 17533707--17533889 Score: 192
Period size: 51 Copynumber: 3.6 Consensus size: 51
17533697 TGAAAGTGAT
* *
17533707 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-ATAATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGTAATA
* * * * ** * *
17533757 GGTCGCATGTGTAGTACTATGTGCAGGCTATTATGCGTACCAAATAGT-TTC
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GTAATA
* * *
17533808 GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAAT-
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GTAATA
* *
17533859 GGTCACATGTATAGTACTATGTGCAAGCTAC
1 GGTCACATGTGTAGTACTATGTGCAGGCTAC
17533890 CATGTGAACC
Statistics
Matches: 105, Mismatches: 25, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
50 37 0.35
51 66 0.63
52 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGTAATA
Found at i:17534035 original size:45 final size:45
Alignment explanation
Indices: 17533897--17534035 Score: 233
Period size: 45 Copynumber: 3.1 Consensus size: 45
17533887 TACCATGTGA
*
17533897 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
1 ACCGGACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
*
17533942 ACCAGACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
1 ACCGGACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
* * *
17533987 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGGACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
17534032 ACCG
1 ACCG
17534036 AGTATCTGTT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
ACCGGACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
Found at i:17534106 original size:23 final size:22
Alignment explanation
Indices: 17534080--17534123 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
17534070 ATTTGACTAA
17534080 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
17534103 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
17534124 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:17537820 original size:16 final size:16
Alignment explanation
Indices: 17537801--17537871 Score: 58
Period size: 16 Copynumber: 4.6 Consensus size: 16
17537791 TATTTGACAA
*
17537801 TTTAAATATAAATTAT
1 TTTATATATAAATTAT
* **
17537817 TTTATTTATATTTTAT
1 TTTATATATAAATTAT
17537833 TTTATATATAAA-TA-
1 TTTATATATAAATTAT
* *
17537847 TTTATTTAT-ATTTAT
1 TTTATATATAAATTAT
17537862 ATTTATATAT
1 -TTTATATAT
17537872 TTTGTTCACT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
13 1 0.02
14 10 0.24
15 2 0.05
16 29 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATATATAAATTAT
Found at i:17537828 original size:6 final size:6
Alignment explanation
Indices: 17537814--17537869 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
17537804 AAATATAAAT
* *
17537814 TATTT- TATTTA TATTT- TATTTTA TATATA AATATT- TATTTA TATTTA
1 TATTTA TATTTA TATTTA TA-TTTA TATTTA TAT-TTA TATTTA TATTTA
17537861 TATTTA TAT
1 TATTTA TAT
17537870 ATTTTGTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
5 9 0.21
6 30 0.71
7 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATTTA
Found at i:17537860 original size:24 final size:23
Alignment explanation
Indices: 17537828--17537873 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
17537818 TTATTTATAT
17537828 TTTATTTTATATATAAATATTTA
1 TTTATTTTATATATAAATATTTA
* *
17537851 TTTATATTTATATTTATATATTT
1 TTTAT-TTTATATATAAATATTT
17537874 TGTTCACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATTTTATATATAAATATTTA
Found at i:17538109 original size:88 final size:87
Alignment explanation
Indices: 17537999--17538626 Score: 398
Period size: 86 Copynumber: 7.3 Consensus size: 87
17537989 TTTTTTAGTG
* * * *
17537999 AATAAAATTTGTTTCGGGATTTATTCTCGCTATTCAACGGATTTTATTCCAATTTTGATTTTATT
1 AATAAAATATGTTTCAGGATTTATTCCCGCTATTCAACGGATTTTATTCC-ATTTTAATTTTATT
* *
17538064 TCTAAAACAAG-TATTAAAATTAA
65 TCTAAAACGAGAAATTAAAATT-A
* * * * * *
17538087 AATAATATATGTTTCATGATTTATTCCTG-TCGTTCAACGGATTTTATTCCTTTTTTATTTTATT
1 AATAAAATATGTTTCAGGATTTATTCCCGCT-ATTCAACGGATTTTATTCCATTTTAATTTTATT
*
17538151 T-TCAAACGAGAAATTAAAATTA
65 TCTAAAACGAGAAATTAAAATTA
** * * * * *
17538173 AATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAATGGA-TTTATTACATTTTCATTTTGTTG
1 AATAAAATATGTTTCAGGATTTATTCCCGCTATTCAACGGATTTTATTCCATTTTAATTTTATTT
* *
17538237 CCAAAGCGAGAAATTAAAATTA
66 CTAAAACGAGAAATTAAAATTA
* * * * *
17538259 AATAAAATCTAT-TTTGA-GATTTATTCCCGCTATTTAACAAGATTTTATTCGATTTTAATTTTG
1 AATAAAA--TATGTTTCAGGATTTATTCCCGCTATTCAAC-GGATTTTATTCCATTTTAATTTTA
* *
17538322 TTTC-CAAACTAG-AATT-AAATTA
63 TTTCTAAAACGAGAAATTAAAATTA
* * * ** * * * * * *
17538344 AATAAAAAATTTTTCAGGATTTATTCCCACCGTTTAACAAGATTTTATTCAATATTGA-TTTGTT
1 AATAAAATATGTTTCAGGATTTATTCCCGCTATTCAAC-GGATTTTATTCCATTTTAATTTTATT
* * * *
17538408 TC-CAAATGA-AGACTT--AATCA
65 TCTAAAACGAGA-AATTAAAATTA
* * * * * * *
17538428 AAT-AACTTTGTTTC-GGTATTTATTCCCG-TCGTTCAATGGATTTTATTACATTTTGATTTTGT
1 AATAAAATATGTTTCAGG-ATTTATTCCCGCT-ATTCAACGGATTTTATTCCATTTTAATTTTAT
*
17538490 TTCCAAAACGAGAAATTAAAATTA
64 TTCTAAAACGAGAAATTAAAATTA
* * ** * * ** *
17538514 AATAAAATATGTTT-TGAGATTTATTCCAGCCGTTTAACAAGATTTTATTTGATTTTAATTTTGT
1 AATAAAATATGTTTCAG-GATTTATTCCCGCTATTCAAC-GGATTTTATTCCATTTTAATTTTAT
* ** *
17538578 TTC-CAAATTAG-AATT-AAATAA
64 TTCTAAAACGAGAAATTAAAATTA
* *
17538599 AATAAAATTTGTTTCGGGATTTATTCCC
1 AATAAAATATGTTTCAGGATTTATTCCC
17538627 TTCGTTTAAC
Statistics
Matches: 432, Mismatches: 83, Indels: 53
0.76 0.15 0.09
Matches are distributed among these distances:
82 17 0.04
83 32 0.07
84 32 0.07
85 98 0.23
86 101 0.23
87 63 0.15
88 89 0.21
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (87 bp):
AATAAAATATGTTTCAGGATTTATTCCCGCTATTCAACGGATTTTATTCCATTTTAATTTTATTT
CTAAAACGAGAAATTAAAATTA
Found at i:17538207 original size:86 final size:86
Alignment explanation
Indices: 17537999--17538668 Score: 535
Period size: 85 Copynumber: 7.8 Consensus size: 86
17537989 TTTTTTAGTG
* * * ** *
17537999 AATAAAATTTGTTTCGGGATTTATTCTCGCTATTCAACGGATTTTATTCCAATTTTGATTTTATT
1 AATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAACGGATTTTATTCC-ATTTTGATTTTGTT
* * *
17538064 TCTAAAACAAG-TATTAAAATTAA
65 TC-CAAACGAGAAATTAAAATT-A
* * * * * * *
17538087 AATAATATATGTTTCATGATTTATTCCTGTCGTTCAACGGATTTTATTCCTTTTTTATTTTATTT
1 AATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAACGGATTTTATTCCATTTTGATTTTGTTT
*
17538152 TCAAACGAGAAATTAAAATTA
66 CCAAACGAGAAATTAAAATTA
* * * *
17538173 AATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAATGGA-TTTATTACATTTTCATTTTGTTG
1 AATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAACGGATTTTATTCCATTTTGATTTTGTTT
17538237 CCAAAGCGAGAAATTAAAATTA
66 CCAAA-CGAGAAATTAAAATTA
* ** * * * *
17538259 AATAAAATCTAT-TTTGA-GATTTATTCCCGCTATTTAACAAGATTTTATTCGATTTTAATTTTG
1 AATAAAA--TATGTTTCAGGATTTATTCCCGCCGTTCAAC-GGATTTTATTCCATTTTGATTTTG
*
17538322 TTTCCAAACTAG-AATT-AAATTA
63 TTTCCAAACGAGAAATTAAAATTA
* * * * * * *
17538344 AATAAAAAATTTTTCAGGATTTATTCCCACCGTTTAACAAGATTTTATTCAATATTGA-TTTGTT
1 AATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAAC-GGATTTTATTCCATTTTGATTTTGTT
* * *
17538408 TCCAAATGA-AGACTT--AATCA
65 TCCAAACGAGA-AATTAAAATTA
* * * * *
17538428 AAT-AACTTTGTTTC-GGTATTTATTCCCGTCGTTCAATGGATTTTATTACATTTTGATTTTGTT
1 AATAAAATATGTTTCAGG-ATTTATTCCCGCCGTTCAACGGATTTTATTCCATTTTGATTTTGTT
17538491 TCCAAAACGAGAAATTAAAATTA
65 TCC-AAACGAGAAATTAAAATTA
* * * * ** *
17538514 AATAAAATATGTTT-TGAGATTTATTCCAGCCGTTTAACAAGATTTTATTTGATTTTAATTTTGT
1 AATAAAATATGTTTCAG-GATTTATTCCCGCCGTTCAAC-GGATTTTATTCCATTTTGATTTTGT
** *
17538578 TTCCAAATTAG-AATT-AAATAA
64 TTCCAAACGAGAAATTAAAATTA
* * ** * * * **
17538599 AATAAAATTTGTTTCGGGATTTATTCCCTTCGTTTAACAAGATTTTATTCGATACTGA-TTTGTT
1 AATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAAC-GGATTTTATTCCATTTTGATTTTGTT
17538663 TCCAAA
65 TCCAAA
17538669 TGAAGACTTA
Statistics
Matches: 475, Mismatches: 86, Indels: 46
0.78 0.14 0.08
Matches are distributed among these distances:
82 17 0.04
83 34 0.07
84 44 0.09
85 126 0.27
86 99 0.21
87 61 0.13
88 94 0.20
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.43
Consensus pattern (86 bp):
AATAAAATATGTTTCAGGATTTATTCCCGCCGTTCAACGGATTTTATTCCATTTTGATTTTGTTT
CCAAACGAGAAATTAAAATTA
Found at i:17538706 original size:255 final size:254
Alignment explanation
Indices: 17538189--17538708 Score: 810
Period size: 255 Copynumber: 2.0 Consensus size: 254
17538179 ATATGTTTCA
*
17538189 GGATTTATTCCCGCCGTTCAATGGATTTATTACATTTTCATTTTGTTGCCAAAGCGAGAAATTAA
1 GGATTTATTCCCGCCGTTCAATGGATTTATTACATTTTCATTTTGTTGCCAAAACGAGAAATTAA
* * *
17538254 AATTAAATAAAATCTATTTTGAGATTTATTCCCGCTATTTAACAAGATTTTATTCGATTTTAATT
66 AATTAAATAAAATATATTTTGAGATTTATTCCAGCCATTTAACAAGATTTTATTCGATTTTAATT
*
17538319 TTGTTTCCAAACTAGAATTAAATTAAATAAAAAATTTTTCAGGATTTATTCCCACCGTTTAACAA
131 TTGTTTCCAAACTAGAATTAAATAAAATAAAAAATTTTTCAGGATTTATTCCCACCGTTTAACAA
* * *
17538384 GATTTTATTCAATATTGATTTGTTTCCAAATGAAGACTTAATCAAATAACTTTGTTTCG
196 GATTTTATTCAATACTGATTTGTTTCCAAATGAAGACTTAATCAAATAACTTTATATCG
* * * *
17538443 GTATTTATTCCCGTCGTTCAATGGATTTTATTACATTTTGATTTTGTTTCCAAAACGAGAAATTA
1 GGATTTATTCCCGCCGTTCAATGGA-TTTATTACATTTTCATTTTGTTGCCAAAACGAGAAATTA
* * *
17538508 AAATTAAATAAAATATGTTTTGAGATTTATTCCAGCCGTTTAACAAGATTTTATTTGATTTTAAT
65 AAATTAAATAAAATATATTTTGAGATTTATTCCAGCCATTTAACAAGATTTTATTCGATTTTAAT
* * * **
17538573 TTTGTTTCCAAATTAGAATTAAATAAAAT-AAAATTTGTTTCGGGATTTATTCCCTTCGTTTAAC
130 TTTGTTTCCAAACTAGAATTAAATAAAATAAAAAATT-TTTCAGGATTTATTCCCACCGTTTAAC
*
17538637 AAGATTTTATTCGATACTGATTTGTTTCCAAATGAAGACTTAATCAAATAA-TTCTATATCG
194 AAGATTTTATTCAATACTGATTTGTTTCCAAATGAAGACTTAATCAAATAACTT-TATATCG
17538698 GGATTTATTCC
1 GGATTTATTCC
17538709 TGACGTTTAA
Statistics
Matches: 241, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
254 31 0.13
255 210 0.87
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (254 bp):
GGATTTATTCCCGCCGTTCAATGGATTTATTACATTTTCATTTTGTTGCCAAAACGAGAAATTAA
AATTAAATAAAATATATTTTGAGATTTATTCCAGCCATTTAACAAGATTTTATTCGATTTTAATT
TTGTTTCCAAACTAGAATTAAATAAAATAAAAAATTTTTCAGGATTTATTCCCACCGTTTAACAA
GATTTTATTCAATACTGATTTGTTTCCAAATGAAGACTTAATCAAATAACTTTATATCG
Found at i:17538716 original size:83 final size:85
Alignment explanation
Indices: 17538291--17538720 Score: 357
Period size: 85 Copynumber: 5.1 Consensus size: 85
17538281 ATTCCCGCTA
* * * *
17538291 TTTAACAAGATTTTATTCGATTTTAATTTTGTTTCCAAACT--AGAATTAAATTAAATAAAAAAT
1 TTTAACAAGATTTTATTCGATATTGATTTTGTTTCCAAA-TGAAGAATTAAATCAAAT--AAATT
* *
17538354 T-TTTCAGGATTTATTCC-CACCG
63 TGTTTCGGGATTTATTCCTGA-CG
* * *
17538376 TTTAACAAGATTTTATTCAATATTGA-TTTGTTTCCAAATGAAGACTT-AATCAAATAACTTTGT
1 TTTAACAAGATTTTATTCGATATTGATTTTGTTTCCAAATGAAGAATTAAATCAAATAAATTTGT
* * *
17538439 TTCGGTATTTATTCCCGTCG
66 TTCGGGATTTATTCCTGACG
* ** * * *
17538459 TTCAA-TGGATTTTATTAC-ATTTTGATTTTGTTTCCAAAACG-AGAAATTAAAATTAAATAAAA
1 TTTAACAAGATTTTATT-CGATATTGATTTTGTTTCC-AAATGAAG-AATT-AAATCAAAT-AAA
* * * * *
17538521 TATGTTTTGAGATTTATTCCAGCCG
61 TTTGTTTCGGGATTTATTCCTGACG
* * * * *
17538546 TTTAACAAGATTTTATTTGATTTTAATTTTGTTTCCAAAT-TAGAATTAAATAAAATAAAATTTG
1 TTTAACAAGATTTTATTCGATATTGATTTTGTTTCCAAATGAAGAATTAAATCAAAT-AAATTTG
*
17538610 TTTCGGGATTTATTCCCT-TCG
65 TTTCGGGATTTATT-CCTGACG
* * *
17538631 TTTAACAAGATTTTATTCGATACTGA-TTTGTTTCCAAATGAAGACTT-AATCAAAT-AATTCTA
1 TTTAACAAGATTTTATTCGATATTGATTTTGTTTCCAAATGAAGAATTAAATCAAATAAATT-TG
*
17538693 TATCGGGATTTATTCCTGACG
65 TTTCGGGATTTATTCCTGACG
17538714 TTTAACA
1 TTTAACA
17538721 TACTTTATTT
Statistics
Matches: 280, Mismatches: 47, Indels: 38
0.77 0.13 0.10
Matches are distributed among these distances:
82 26 0.09
83 56 0.20
84 46 0.16
85 84 0.30
86 13 0.05
87 30 0.11
88 25 0.09
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (85 bp):
TTTAACAAGATTTTATTCGATATTGATTTTGTTTCCAAATGAAGAATTAAATCAAATAAATTTGT
TTCGGGATTTATTCCTGACG
Found at i:17538747 original size:59 final size:59
Alignment explanation
Indices: 17538684--17538795 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
17538674 ACTTAATCAA
* * * * *
17538684 ATAATTCTATATCGGGATTTATTCCTGAC-GTTTAACATACTTTATTTTGATTTAATTAC
1 ATAATTCTATATCGAGATTTAATCCTG-CTGTTTAACAAAATTGATTTTGATTTAATTAC
* *
17538743 ATAATTTTATTTCGAGATTTAATCCTGCTGTTTAACAAAATTGATTTTGATTT
1 ATAATTCTATATCGAGATTTAATCCTGCTGTTTAACAAAATTGATTTTGATTT
17538796 TGTTTTAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 1 0.02
59 44 0.98
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (59 bp):
ATAATTCTATATCGAGATTTAATCCTGCTGTTTAACAAAATTGATTTTGATTTAATTAC
Found at i:17539414 original size:13 final size:13
Alignment explanation
Indices: 17539396--17539420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17539386 CTTAAGCTTC
17539396 AAAATGTGTTGTG
1 AAAATGTGTTGTG
17539409 AAAATGTGTTGT
1 AAAATGTGTTGT
17539421 ATGTGCCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (13 bp):
AAAATGTGTTGTG
Found at i:17544092 original size:15 final size:15
Alignment explanation
Indices: 17544050--17544104 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
17544040 TAATCCAATT
17544050 GAAAAAGAA-AAAGAA
1 GAAAAAGAAGAAA-AA
* **
17544065 GTTAAAA-AAGAAATT
1 G-AAAAAGAAGAAAAA
17544080 GAAAAAGAAGAAAAA
1 GAAAAAGAAGAAAAA
17544095 GAAAAAGAAG
1 GAAAAAGAAG
17544105 TTGAAAAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
14 4 0.13
15 20 0.65
16 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
GAAAAAGAAGAAAAA
Found at i:17544110 original size:12 final size:12
Alignment explanation
Indices: 17544056--17544114 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
17544046 AATTGAAAAA
17544056 GAAAAAGAAGTT
1 GAAAAAGAAGTT
* *
17544068 AAAAAAGAAATT
1 GAAAAAGAAGTT
**
17544080 GAAAAAGAAGAAAAA
1 GAAAAAGAAG---TT
17544095 GAAAAAGAAGTT
1 GAAAAAGAAGTT
17544107 GAAAAAGA
1 GAAAAAGA
17544115 GACAAAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
12 26 0.72
15 10 0.28
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.10
Consensus pattern (12 bp):
GAAAAAGAAGTT
Found at i:17552723 original size:28 final size:31
Alignment explanation
Indices: 17552650--17552728 Score: 83
Period size: 32 Copynumber: 2.6 Consensus size: 31
17552640 TTGGTTCAAA
*
17552650 TATTTGACAGTTTAAATATAAATTATCTTATT
1 TATTT-ACAGTTTATATATAAATTATCTTATT
** *
17552682 TATATTTTATTTTATATATAAA-TAT-TTATT
1 TAT-TTACAGTTTATATATAAATTATCTTATT
17552712 TATTTACA-TTTATATAT
1 TATTTACAGTTTATATAT
17552729 TTTGTCCATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
28 9 0.22
29 3 0.08
30 8 0.20
31 3 0.08
32 15 0.38
33 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTTACAGTTTATATATAAATTATCTTATT
Found at i:17553715 original size:13 final size:13
Alignment explanation
Indices: 17553697--17553726 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
17553687 AGCCCAAACT
17553697 CAATTACCCAACC
1 CAATTACCCAACC
17553710 CAATTACCCAACC
1 CAATTACCCAACC
17553723 CAAT
1 CAAT
17553727 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:17553877 original size:9 final size:9
Alignment explanation
Indices: 17553865--17553923 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
17553855 AAATAAAAAA
17553865 AATTCGGGT
1 AATTCGGGT
*
17553874 AATTTGGGT
1 AATTCGGGT
*
17553883 ATTTTTC-GGT
1 A--ATTCGGGT
17553893 AATTCGGGT
1 AATTCGGGT
17553902 AATTCGGGT
1 AATTCGGGT
17553911 AATTCGGGT
1 AATTCGGGT
17553920 AATT
1 AATT
17553924 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.07
9 34 0.79
10 4 0.09
11 2 0.05
ACGTcount: A:0.22, C:0.08, G:0.29, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:17555177 original size:19 final size:17
Alignment explanation
Indices: 17555147--17555184 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
17555137 ATTTTTTTTT
17555147 AAAAAAAAAGTAAATTA
1 AAAAAAAAAGTAAATTA
17555164 AAAACAAAAGAGTAAATTA
1 AAAA-AAAA-AGTAAATTA
17555183 AA
1 AA
17555185 GAATATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (17 bp):
AAAAAAAAAGTAAATTA
Found at i:17562745 original size:50 final size:50
Alignment explanation
Indices: 17562632--17562922 Score: 359
Period size: 50 Copynumber: 5.7 Consensus size: 50
17562622 GATAATAACA
* * **
17562632 TGCCAAAGCCATGTCCCAGACATGGTATTACATGGGATATTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
17562683 TGCCAACTCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATCTCGG
*
17562733 TGCGAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
17562783 TGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCACTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
17562833 TGCCAACACGATGTCTCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
*
17562889 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
17562923 AGGTCTCTTT
Statistics
Matches: 206, Mismatches: 26, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
50 138 0.67
51 32 0.16
53 5 0.02
56 31 0.15
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:17569195 original size:32 final size:32
Alignment explanation
Indices: 17569154--17569217 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
17569144 ACTATAAAGA
17569154 ACAAATATCCACTGCCTAGAATTGATGATCTG
1 ACAAATATCCACTGCCTAGAATTGATGATCTG
17569186 ACAAATATCCACTGCCTAGAATTGATGATCTG
1 ACAAATATCCACTGCCTAGAATTGATGATCTG
17569218 TTTGACCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (32 bp):
ACAAATATCCACTGCCTAGAATTGATGATCTG
Found at i:17579604 original size:32 final size:32
Alignment explanation
Indices: 17579566--17579632 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
17579556 AAACATTAAT
*
17579566 ATAAACATAACATAATCAATTCCTATACATGC
1 ATAAACATAACATAATCAATTCATATACATGC
*
17579598 ATAAACATAGCATAATCAATTCATATACATGC
1 ATAAACATAACATAATCAATTCATATACATGC
17579630 ATA
1 ATA
17579633 TTGTCCCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.28
Consensus pattern (32 bp):
ATAAACATAACATAATCAATTCATATACATGC
Found at i:17581037 original size:2 final size:2
Alignment explanation
Indices: 17581030--17581062 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17581020 AATTGGAATT
17581030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17581063 CATACATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17581714 original size:41 final size:41
Alignment explanation
Indices: 17581669--17581779 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 41
17581659 TATCTGAGTT
* * *
17581669 ATTCAGGCTCTGTGCCTAGCAGGCTTAATGCCAGTGATATA
1 ATTCAGACTCTGCGCCTAGCAGGCTTAATGCCAGTGAAATA
* * *
17581710 ATTCAGACTTTGCGTCTAGCAGGCTTAATGCCGGTGAAATA
1 ATTCAGACTCTGCGCCTAGCAGGCTTAATGCCAGTGAAATA
* * * * *
17581751 TTTCAGACTTTACGTCTAGCACGCTTAAT
1 ATTCAGACTCTGCGCCTAGCAGGCTTAAT
17581780 ACCGGTGTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (41 bp):
ATTCAGACTCTGCGCCTAGCAGGCTTAATGCCAGTGAAATA
Found at i:17581785 original size:41 final size:41
Alignment explanation
Indices: 17581684--17581786 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
17581674 GGCTCTGTGC
* * *
17581684 CTAGCAGGCTTAATGCCAGTGATATAATTCAGACTTTGCGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTACGT
*
17581725 CTAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTACGT
* *
17581766 CTAGCACGCTTAATACCGGTG
1 CTAGCAGGCTTAATGCCGGTG
17581787 TTCTGTATCA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTACGT
Found at i:17582513 original size:14 final size:14
Alignment explanation
Indices: 17582494--17582520 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17582484 ATGATTAATA
17582494 GTATATACGTATAT
1 GTATATACGTATAT
17582508 GTATATACGTATA
1 GTATATACGTATA
17582521 AAGATGTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
GTATATACGTATAT
Found at i:17591579 original size:41 final size:41
Alignment explanation
Indices: 17591474--17591584 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 41
17591464 TCTAAAGTGT
* *
17591474 AAACAGGGGCACTTATGTGCAATTCAGGGGTACCGAAGTAC
1 AAACAGAGGCACATATGTGCAATTCAGGGGTACCGAAGTAC
** * * **
17591515 AAACA-ATCTCACATACGTACAATTCAGGGGTATGGAAGTAC
1 AAACAGA-GGCACATATGTGCAATTCAGGGGTACCGAAGTAC
*
17591556 AAACAGAGGCACGTATGTGCAATTCAGGG
1 AAACAGAGGCACATATGTGCAATTCAGGG
17591585 AATAATTAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 54 0.98
42 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (41 bp):
AAACAGAGGCACATATGTGCAATTCAGGGGTACCGAAGTAC
Found at i:17594813 original size:18 final size:18
Alignment explanation
Indices: 17594790--17594824 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17594780 ACGATGTGCC
17594790 AAACTATTTTCATGCTTG
1 AAACTATTTTCATGCTTG
*
17594808 AAACTATTTTGATGCTT
1 AAACTATTTTCATGCTT
17594825 ATTGTTCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (18 bp):
AAACTATTTTCATGCTTG
Found at i:17597746 original size:13 final size:13
Alignment explanation
Indices: 17597728--17597753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17597718 ATAGTCACTG
17597728 AAATTATTATAAT
1 AAATTATTATAAT
17597741 AAATTATTATAAT
1 AAATTATTATAAT
17597754 TAAGATTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTATAAT
Found at i:17602392 original size:22 final size:22
Alignment explanation
Indices: 17602337--17602394 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
17602327 CAGCCCGAAT
* *
17602337 TATATATTAAATATTTTTTTTA
1 TATATATTAAATATCTATTTTA
* *
17602359 T-TTTAATCAAATATCTATTTTA
1 TATAT-ATTAAATATCTATTTTA
17602381 TATATATTAAATAT
1 TATATATTAAATAT
17602395 ATGTATTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
21 2 0.07
22 24 0.86
23 2 0.07
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATATTAAATATCTATTTTA
Found at i:17607386 original size:48 final size:47
Alignment explanation
Indices: 17607310--17607467 Score: 147
Period size: 48 Copynumber: 3.3 Consensus size: 47
17607300 AACAGATTTC
* * * * * * *
17607310 TCGGTGGCCTACACACAATCTGTACCACCTTTATGTAATAACAGACTC
1 TCGGTGGCCTGCACACAGTCCGTGCCACC-TTATGTATTAACAGAATA
* *
17607358 TCGGTGGCCTGCACATAGTCCGTGCCACCCT-TGTACCTTAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCTTATGTA--TTAACAGAATA
* * * *
17607406 TTGGTGGTCTGCACACAGTCCGTGCCACCCTTATATCTTAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCA-CCTTATGTATTAACAGAATA
*
17607454 TTGGTGGCCTGCAC
1 TCGGTGGCCTGCAC
17607468 CCTTGTATCT
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
46 4 0.04
47 1 0.01
48 80 0.89
49 3 0.03
50 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (47 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCTTATGTATTAACAGAATA
Found at i:17607477 original size:34 final size:34
Alignment explanation
Indices: 17607431--17607501 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
17607421 CAGTCCGTGC
17607431 CACCCTTATATCTTAACAGAATATTGGTGGCCTG
1 CACCCTTATATCTTAACAGAATATTGGTGGCCTG
* *
17607465 CACCCTTGTATCTTAATAGAATATTGGTGGCCTG
1 CACCCTTATATCTTAACAGAATATTGGTGGCCTG
17607499 CAC
1 CAC
17607502 ACAGTCCGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (34 bp):
CACCCTTATATCTTAACAGAATATTGGTGGCCTG
Found at i:17611505 original size:30 final size:30
Alignment explanation
Indices: 17611370--17611506 Score: 100
Period size: 30 Copynumber: 4.6 Consensus size: 30
17611360 ACAAAAATAT
* * *
17611370 AAATTACATTTTAGCCCCTAAACTTTTCAA
1 AAATTACATTTTGGCCCCTAAAATTTTTAA
* * *
17611400 AAATTACATTTTGACACCT-AAATTTTTCTA
1 AAATTACATTTTGGCCCCTAAAATTTTT-AA
* * ** * *
17611430 AATTTGCATGATGACCCCTAATATTTTGT--
1 AAATTACATTTTGGCCCCTAAAATTTT-TAA
* **
17611459 AAATTATATTCGGGCCCCTAAAATTTTTAA
1 AAATTACATTTTGGCCCCTAAAATTTTTAA
17611489 AAATTACATTTTGGCCCC
1 AAATTACATTTTGGCCCC
17611507 ATATTTTCCT
Statistics
Matches: 79, Mismatches: 23, Indels: 10
0.71 0.21 0.09
Matches are distributed among these distances:
28 1 0.01
29 25 0.32
30 46 0.58
31 6 0.08
32 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.39
Consensus pattern (30 bp):
AAATTACATTTTGGCCCCTAAAATTTTTAA
Found at i:17612185 original size:19 final size:19
Alignment explanation
Indices: 17612138--17612191 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 19
17612128 CAAGAAGTGA
*
17612138 AAAAAGAAAAAAACAGCCAG
1 AAAAA-AAAAAAACAGCAAG
*
17612158 AAAAGAAAAAAAATAGCAAGG
1 AAAA-AAAAAAAACAGCAA-G
17612179 AAAAAAAGAAAAA
1 AAAAAAA-AAAAA
17612192 AAACAAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAACAGCAAG
Found at i:17612204 original size:21 final size:23
Alignment explanation
Indices: 17612158--17612211 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
17612148 AAACAGCCAG
*
17612158 AAAAGAAAAAAAATAGCAAGGAAA
1 AAAAGAAAAAAAACA-CAAGGAAA
17612182 AAAAGAAAAAAAACA-AAGG-AA
1 AAAAGAAAAAAAACACAAGGAAA
17612203 AAAAGAAAA
1 AAAAGAAAA
17612212 GAAAGGGGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 11 0.38
22 4 0.14
24 14 0.48
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.02
Consensus pattern (23 bp):
AAAAGAAAAAAAACACAAGGAAA
Found at i:17612313 original size:4 final size:4
Alignment explanation
Indices: 17612304--17612393 Score: 57
Period size: 4 Copynumber: 22.5 Consensus size: 4
17612294 CTGAACGGGG
*
17612304 AAGA AAGA AAGAA AAGA GAAGA AAGA AAGA AGGA GAA-A AA-A AAGA AAG-
1 AAGA AAGA AAG-A AAGA -AAGA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA
* *
17612352 AAG- AAGG AAG- AAGA AAGGGA AAGA AA-A AAGGA AAAA AAGA AA
1 AAGA AAGA AAGA AAGA AA--GA AAGA AAGA AA-GA AAGA AAGA AA
17612394 AAATTAAGTA
Statistics
Matches: 72, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
3 17 0.24
4 39 0.54
5 12 0.17
6 4 0.06
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:17612344 original size:26 final size:26
Alignment explanation
Indices: 17612315--17612391 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 26
17612305 AGAAAGAAAG
17612315 AAAAGAGAAGAAAGAAAGAAGGAG-A
1 AAAAGAGAAGAAAGAAAGAAGGAGAA
17612340 AAAA-A-AAGAAAG-AAGAAGGAAGAA
1 AAAAGAGAAGAAAGAAAGAAGG-AGAA
* *
17612364 GAAAG-G--GAAAGAAAAAAGGA-AA
1 AAAAGAGAAGAAAGAAAGAAGGAGAA
17612386 AAAAGA
1 AAAAGA
17612392 AAAAATTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
22 13 0.30
23 15 0.35
24 11 0.26
25 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (26 bp):
AAAAGAGAAGAAAGAAAGAAGGAGAA
Found at i:17612348 original size:33 final size:33
Alignment explanation
Indices: 17612306--17612379 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
17612296 GAACGGGGAA
*
17612306 GAAAGAAAGA-AAAG-AGAAGAAAGAA-AGAAGG
1 GAAAGAAAAAGAAAGAAGAAGAAAGAAGA-AAGG
*
17612337 AGAAA-AAAAAGAAAGAAGAAGGAAGAAGAAAGG
1 -GAAAGAAAAAGAAAGAAGAAGAAAGAAGAAAGG
17612370 GAAAGAAAAA
1 GAAAGAAAAA
17612380 AGGAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
31 4 0.11
32 12 0.33
33 19 0.53
34 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (33 bp):
GAAAGAAAAAGAAAGAAGAAGAAAGAAGAAAGG
Found at i:17612349 original size:19 final size:19
Alignment explanation
Indices: 17612307--17612357 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
17612297 AACGGGGAAG
* *
17612307 AAAGAAAGAA-AAGAGAAG
1 AAAGAAAGAAGAAGAAAAA
*
17612325 AAAGAAAGAAGGAGAAAAA
1 AAAGAAAGAAGAAGAAAAA
17612344 AAAGAAAGAAGAAG
1 AAAGAAAGAAGAAG
17612358 GAAGAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAGAAGAAAAA
Found at i:17612380 original size:37 final size:37
Alignment explanation
Indices: 17612307--17612393 Score: 93
Period size: 43 Copynumber: 2.2 Consensus size: 37
17612297 AACGGGGAAG
*
17612307 AAAGAAAGAAAAGAGAAGAAAGAAAGAAGGAGAAAAA
1 AAAGAAAGAAAAGAGAAGAAAGAAAGAAAGAGAAAAA
* *
17612344 AAAGAAAGAAGAAGGAAGAAGAAAGGGAAAGAAAAAAGGAAAA
1 AAAGAAAGAA-AA-G-AGAAGAAA--GAAAG-AAAGAGAAAAA
17612387 AAAGAAA
1 AAAGAAA
17612394 AAATTAAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 10 0.24
38 2 0.05
39 1 0.02
40 8 0.20
42 5 0.12
43 15 0.37
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (37 bp):
AAAGAAAGAAAAGAGAAGAAAGAAAGAAAGAGAAAAA
Found at i:17612585 original size:17 final size:17
Alignment explanation
Indices: 17612544--17612607 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 17
17612534 AAAGGCCCAA
17612544 CAACGCAGCAGTAGGCCC
1 CAACGCAGCAGTAGG-CC
17612562 AACAACGCAGCAGTAGGCC
1 --CAACGCAGCAGTAGGCC
*
17612581 CAACGCAGCAGCAGG-C
1 CAACGCAGCAGTAGGCC
*
17612597 CAACCCAGCAG
1 CAACGCAGCAG
17612608 GCCCACAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.26
17 14 0.33
19 2 0.05
20 15 0.36
ACGTcount: A:0.33, C:0.38, G:0.27, T:0.03
Consensus pattern (17 bp):
CAACGCAGCAGTAGGCC
Found at i:17612594 original size:20 final size:20
Alignment explanation
Indices: 17612536--17612584 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
17612526 ATTCCAGCAA
17612536 AGGCCCAACAACGCAGCAGT
1 AGGCCCAACAACGCAGCAGT
17612556 AGGCCCAACAACGCAGCAGT
1 AGGCCCAACAACGCAGCAGT
17612576 AGGCCCAAC
1 AGGCCCAAC
17612585 GCAGCAGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.37, G:0.24, T:0.04
Consensus pattern (20 bp):
AGGCCCAACAACGCAGCAGT
Found at i:17613244 original size:18 final size:17
Alignment explanation
Indices: 17613211--17613298 Score: 79
Period size: 18 Copynumber: 4.9 Consensus size: 17
17613201 TCAAAAACAA
17613211 ATTCGTGTTTCAAAAAT
1 ATTCGTGTTTCAAAAAT
17613228 ATTCGTGTTTTCAAAAAT
1 ATTCGTG-TTTCAAAAAT
* *
17613246 -TCCCGTGTTTCACAAAT
1 AT-TCGTGTTTCAAAAAT
* *
17613263 TTTTGTGTTTTCAAAAATT
1 ATTCGTG-TTTCAAAAA-T
17613282 ATTATCGTGTTTCAAAA
1 A-T-TCGTGTTTCAAAA
17613299 TTCTCATGGC
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
17 20 0.35
18 23 0.40
19 1 0.02
20 9 0.16
21 4 0.07
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (17 bp):
ATTCGTGTTTCAAAAAT
Found at i:17613253 original size:35 final size:35
Alignment explanation
Indices: 17613214--17613281 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
17613204 AAAACAAATT
17613214 CGTGTTTCAAAAATATTCGTGTTTTCAAAAATTCC
1 CGTGTTTCAAAAATATTCGTGTTTTCAAAAATTCC
* * *
17613249 CGTGTTTCACAAATTTTTGTGTTTTCAAAAATT
1 CGTGTTTCAAAAATATTCGTGTTTTCAAAAATT
17613282 ATTATCGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (35 bp):
CGTGTTTCAAAAATATTCGTGTTTTCAAAAATTCC
Found at i:17624328 original size:7 final size:8
Alignment explanation
Indices: 17624306--17624337 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
17624296 TTATGCCTAA
17624306 AAAAACAAC
1 AAAAA-AAC
17624315 AAAAAAAC
1 AAAAAAAC
17624323 AAAAAAAC
1 AAAAAAAC
17624331 AAAAAAA
1 AAAAAAA
17624338 AGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:17624345 original size:19 final size:19
Alignment explanation
Indices: 17624304--17624346 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
17624294 TATTATGCCT
*
17624304 AAAAAAACAACAAAAAAAC
1 AAAAAAACAACAAAAAAAA
17624323 AAAAAAACAA-AAAAAAGAA
1 AAAAAAACAACAAAAAA-AA
17624342 AAAAA
1 AAAAA
17624347 TCAAGATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAACAACAAAAAAAA
Found at i:17625483 original size:78 final size:78
Alignment explanation
Indices: 17625209--17626082 Score: 1169
Period size: 78 Copynumber: 11.3 Consensus size: 78
17625199 GAATTATATT
* *
17625209 TTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAT
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
17625272 ATACCGAGGTATC
66 ATGCCGAGGTATC
* *
17625285 -TGCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCAC
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
17625347 --GCTGAGGTAT-
66 ATGCCGAGGTATC
* *
17625357 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGTCAC
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
17625422 ATGCCGAGGTATC
66 ATGCCGAGGTATC
* *
17625435 TTT-AATTTCTTTTTTTCAAAAAAATTCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTCAATTTCTGTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
17625499 CATGCCGAGGTATC
65 CATGCCGAGGTATC
* * *
17625513 TTT-AATTTTTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCGGGTCAC
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
17625577 ATGCCGAGGTATTTC
66 ATGCCGAGGTA--TC
* * *
17625592 TTTTCAATTTCTGTTTTTCAAAAAAATCAATTCATATTGCGATAGGTGAGTTAAGCCTCGGGTCA
1 -TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
17625657 CATGCCGAGGTATC
65 CATGCCGAGGTATC
* *
17625671 TTT-AATTTCTGTTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCTTCGGGTCA
1 TTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
17625735 CATGCCGAGGTATC
65 CATGCCGAGGTATC
* *
17625749 TTT-AATTT-TGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTTGGGTCAC
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
17625812 ATGCCGAGGTATTTC
66 ATGCCGAGGTA--TC
*
17625827 TTTTCAATTTCTATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 -TTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
17625892 ACATGCCGAGGTATTTC
64 ACATGCCGAGGTA--TC
* * * *
17625909 TTTTAAATTTCTATTTTTCAAAAAAAATCAACTTATATTGC-A-A---GAGGTGAG-CTCGGGTC
1 -TTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
17625968 ACATGCCGAGGTATTTC
64 ACATGCCGAGGTA--TC
* * * *
17625985 TCTTAAATTTCTATTTTTC--AAAAATGAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCA
1 T-TTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
17626048 CATGCCGAGATATT
65 CATGCCGAGGTATC
*
17626062 TTTCAATTTCTATTTTTCAAA
1 TTTCAATTTCTGTTTTTCAAA
17626083 GGTCAACTCA
Statistics
Matches: 727, Mismatches: 44, Indels: 52
0.88 0.05 0.06
Matches are distributed among these distances:
73 40 0.06
74 1 0.00
75 102 0.14
76 113 0.16
77 109 0.15
78 153 0.21
79 27 0.04
80 9 0.01
81 74 0.10
82 99 0.14
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (78 bp):
TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
ATGCCGAGGTATC
Found at i:17625667 original size:236 final size:233
Alignment explanation
Indices: 17625213--17626082 Score: 1207
Period size: 236 Copynumber: 3.7 Consensus size: 233
17625203 TATATTTTTC
* * * *
17625213 AATTTCTGTTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCATATA
1 AATTTCTGTTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATG
** * *
17625275 CCGAGGTATCTGCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC
66 CCGAGGTATCTTTAATTTCTGTTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTC
* * *
17625340 GGGTCAC--GCTGAGGTA---TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGA
131 GGGTCACATGCCGAGGTATTTTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGA
*
17625400 GGTGAGTTGAGCCTTGGGTCACATGCCGAGGTATCTTT
196 GGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATCTTT
* *
17625438 AATTTCTTTTTTTCAAAAAAATTCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATG
1 AATTTCTGTTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATG
* *
17625503 CCGAGGTATCTTTAATTTTTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCC
66 CCGAGGTATCTTTAATTTCTGTTTTTC--AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCC
* *
17625568 TCGGGTCACATGCCGAGGTATTTCTTTTCAATTTCTGTTTTTCAAAAAAATCAATTCATATTGCG
129 TCGGGTCACATGCCGAGGTATTT-TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCG
* *
17625633 ATAGGTGAGTTAAGCCTCGGGTCACATGCCGAGGTATCTTT
193 AGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATCTTT
*
17625674 AATTTCTGTTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCTTCGGGTCACATG
1 AATTTCTGTTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATG
17625739 CCGAGGTATCTTTAATTT-TGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCC
66 CCGAGGTATCTTTAATTTCTGTTTTTC--AAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCC
*
17625803 TTGGGTCACATGCCGAGGTATTTCTTTTCAATTTCTATTTTTCAAAAAAAATCAACTCATATTGC
129 TCGGGTCACATGCCGAGGTATTT-TTTTCAATTTCTATTTTTC-AAAAAAATCAACTCATATTGC
17625868 GAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTCTTTT
192 GAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA--TC-TTT
* * * *
17625913 AAATTTCTATTTTTCAAAAAAAATCAACTTATATTGC-A-A---GAGGTGAG-CTCGGGTCACAT
1 -AATTTCTGTTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACAT
* * * *
17625972 GCCGAGGTATTTCTCTTAAATTTCTATTTTTCAAAAATGAACTCATATTACGAGAGGTGAGTTGA
65 GCCGAGGTA--TCT-TT-AATTTCTGTTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGA
*
17626037 GCCTCGGGTCACATGCCGA-G-ATATTTTTCAATTTCTATTTTTCAAA
126 GCCTCGGGTCACATGCCGAGGTATTTTTTTCAATTTCTATTTTTCAAA
17626083 GGTCAACTCA
Statistics
Matches: 586, Mismatches: 38, Indels: 34
0.89 0.06 0.05
Matches are distributed among these distances:
225 13 0.02
228 67 0.11
230 42 0.07
232 8 0.01
233 3 0.01
234 39 0.07
235 96 0.16
236 216 0.37
237 50 0.09
238 8 0.01
239 11 0.02
240 33 0.06
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (233 bp):
AATTTCTGTTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATG
CCGAGGTATCTTTAATTTCTGTTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTC
GGGTCACATGCCGAGGTATTTTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGA
GGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATCTTT
Found at i:17625684 original size:158 final size:156
Alignment explanation
Indices: 17625209--17626082 Score: 1169
Period size: 158 Copynumber: 5.6 Consensus size: 156
17625199 GAATTATATT
* *
17625209 TTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAT
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* * *
17625272 ATACCGAGGTATC-TGCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAAGTGAGTTG
66 ATGCCGAGGTATCTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
*
17625334 AGCCTCGGGTCAC--GCTGAGGTAT-
131 AGCCTCGGGTCACATGCCGAGGTATC
* *
17625357 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTGGGTCAC
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
17625422 ATGCCGAGGTATCTTT-AATTTCTTTTTTTCAAAAAAATTCAACTCATAATGCGAGAGGTGAGTT
66 ATGCCGAGGTATCTTTCAATTTCTGTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTT
17625486 GAGCCTCGGGTCACATGCCGAGGTATC
130 GAGCCTCGGGTCACATGCCGAGGTATC
* * *
17625513 TTT-AATTTTTGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTAAGTTGAGCCTCGGGTCAC
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
17625577 ATGCCGAGGTATTTCTTTTCAATTTCTGTTTTTCAAAAAAATCAATTCATATTGCGATAGGTGAG
66 ATGCCGAGGTA--TC-TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAG
*
17625642 TTAAGCCTCGGGTCACATGCCGAGGTATC
128 TTGAGCCTCGGGTCACATGCCGAGGTATC
* *
17625671 TTT-AATTTCTGTTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCTTCGGGTCA
1 TTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
17625735 CATGCCGAGGTATCTTT-AATTT-TGTTTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTT
65 CATGCCGAGGTATCTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
*
17625798 GAGCCTTGGGTCACATGCCGAGGTATTTC
130 GAGCCTCGGGTCACATGCCGAGGTA--TC
*
17625827 TTTTCAATTTCTATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 -TTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
* * *
17625892 ACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAAAAATCAACTTATATTGC-A-A---
64 ACATGCCGAGGTA--TC-TTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGT
*
17625952 GAGGTGAG-CTCGGGTCACATGCCGAGGTATTTC
125 GAGTTGAGCCTCGGGTCACATGCCGAGGTA--TC
* * * *
17625985 TCTTAAATTTCTATTTTTC--AAAAATGAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCA
1 T-TTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* * *
17626048 CATGCCGAGATATTTTTCAATTTCTATTTTTCAAA
65 CATGCCGAGGTATCTTTCAATTTCTGTTTTTCAAA
17626083 GGTCAACTCA
Statistics
Matches: 659, Mismatches: 42, Indels: 47
0.88 0.06 0.06
Matches are distributed among these distances:
148 18 0.03
150 66 0.10
151 4 0.01
152 22 0.03
153 39 0.06
154 61 0.09
155 135 0.20
156 8 0.01
157 8 0.01
158 178 0.27
159 82 0.12
160 2 0.00
161 3 0.00
162 6 0.01
163 8 0.01
164 19 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (156 bp):
TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
ATGCCGAGGTATCTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
AGCCTCGGGTCACATGCCGAGGTATC
Found at i:17626496 original size:30 final size:30
Alignment explanation
Indices: 17626431--17626531 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
17626421 TACAAAAACA
* * **
17626431 TAAATTACATTTT-AGCCCCTAAACTTTTCA
1 TAAATTACATTTTGA-CCCTTAAATTTTTTT
*
17626461 AAAATTACATTTTGACCCTTAAATTTTTTT
1 TAAATTACATTTTGACCCTTAAATTTTTTT
* * *
17626491 TAAATTTGCATCTTGACCCTT-AATATTTTT
1 TAAA-TTACATTTTGACCCTTAAATTTTTTT
17626521 TAAATTACATT
1 TAAATTACATT
17626532 CGGGCCCTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
29 5 0.09
30 38 0.66
31 15 0.26
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.47
Consensus pattern (30 bp):
TAAATTACATTTTGACCCTTAAATTTTTTT
Found at i:17626590 original size:29 final size:29
Alignment explanation
Indices: 17626522--17626591 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
17626512 AATATTTTTT
**
17626522 AAATTACATTCGGGCCCTAAAATTTCTAG
1 AAATTACATTTTGGCCCTAAAATTTCTAG
* *
17626551 AAATTACATTTTGGCCCTATATTTTCCTA-
1 AAATTACATTTTGGCCCTAAAATTT-CTAG
17626580 AAATTACATTTT
1 AAATTACATTTT
17626592 TACTCTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 33 0.92
30 3 0.08
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTGGCCCTAAAATTTCTAG
Found at i:17627230 original size:17 final size:17
Alignment explanation
Indices: 17627208--17627246 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
17627198 GTGATAAAAG
17627208 AAAAAAAATAGCAA-GA
1 AAAAAAAATAGCAAGGA
17627224 AAAAAAAATAGCAAGGA
1 AAAAAAAATAGCAAGGA
17627241 AAAAAA
1 AAAAAA
17627247 GAAAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.77, C:0.05, G:0.13, T:0.05
Consensus pattern (17 bp):
AAAAAAAATAGCAAGGA
Found at i:17627246 original size:20 final size:20
Alignment explanation
Indices: 17627203--17627271 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
17627193 AAGAAGTGAT
17627203 AAAAGAAAAAAAATAGCAA-G
1 AAAA-AAAAAAAATAGCAAGG
17627223 ---AAAAAAAAATAGCAAGG
1 AAAAAAAAAAAATAGCAAGG
*
17627240 AAAAAAAGAAAAA-AACAAAGG
1 AAAAAAA-AAAAATAGC-AAGG
17627261 AAAAAAGAAAA
1 AAAAAA-AAAA
17627272 GAAATGGGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
16 14 0.34
17 2 0.05
20 6 0.15
21 18 0.44
22 1 0.02
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAAAATAGCAAGG
Found at i:17627373 original size:4 final size:4
Alignment explanation
Indices: 17627364--17627434 Score: 58
Period size: 4 Copynumber: 17.5 Consensus size: 4
17627354 TTGAACGGGG
* *
17627364 AAGA AAGA AAGA AAGAA AAGA GAAGA AAGA AATA AGGAGA AAAA AAGA
1 AAGA AAGA AAGA AAG-A AAGA -AAGA AAGA AAGA A--AGA AAGA AAGA
*
17627412 AAG- AAG- AAGG AAGA AA-A AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
17627435 AAATTATTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
3 9 0.16
4 36 0.64
5 8 0.14
6 3 0.05
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:17627388 original size:22 final size:22
Alignment explanation
Indices: 17627363--17627434 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
17627353 GTTGAACGGG
17627363 GAAGAAAGAAAGAA-AGAAAAGA
1 GAAGAAAGAAAGAAGAGAAAA-A
*
17627385 GAAGAAAGAAATAAGGAGAAAAA
1 GAAGAAAGAAAGAA-GAGAAAAA
17627408 -AAGAAAG-AAGAAG-GAAGAAA
1 GAAGAAAGAAAGAAGAGAA-AAA
*
17627428 AAAGAAA
1 GAAGAAA
17627435 AAATTATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
19 3 0.07
20 4 0.09
21 10 0.23
22 20 0.45
23 1 0.02
24 6 0.14
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.01
Consensus pattern (22 bp):
GAAGAAAGAAAGAAGAGAAAAA
Found at i:17627747 original size:12 final size:13
Alignment explanation
Indices: 17627716--17627748 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17627706 CCAATCCAGC
17627716 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
17627729 AAAAAAAAAAG-G
1 AAAAAAAAAAGAG
*
17627741 AAGAAAAA
1 AAAAAAAA
17627749 GGAGAAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:17628292 original size:18 final size:18
Alignment explanation
Indices: 17628271--17628369 Score: 103
Period size: 18 Copynumber: 5.6 Consensus size: 18
17628261 AAAATTCATG
*
17628271 TTTCAAAAATCTTCGTGT
1 TTTCAAAAATTTTCGTGT
*
17628289 TTTCAAAAATTTTGGTG-
1 TTTCAAAAATTTTCGTGT
* *
17628306 TTTCTAAAATTTTCATGT
1 TTTCAAAAATTTTCGTGT
* **
17628324 TTTCAACAATTCCCGTG-
1 TTTCAAAAATTTTCGTGT
* *
17628341 TTTCACAAATTTTTGTGT
1 TTTCAAAAATTTTCGTGT
17628359 TTTCAAAAATT
1 TTTCAAAAATT
17628370 ATTATCGTGT
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
17 26 0.41
18 37 0.59
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.47
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:17628297 original size:35 final size:35
Alignment explanation
Indices: 17628248--17628329 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
17628238 TGAAAAATTA
17628248 GTGTTTTCAAAAAAAAATTCATGTTTCAAAAATCTTC
1 GTGTTTTC--AAAAAAATTCATGTTTCAAAAATCTTC
** ** * *
17628285 GTGTTTTCAAAAATTTTGGTGTTTCTAAAATTTTC
1 GTGTTTTCAAAAAAATTCATGTTTCAAAAATCTTC
*
17628320 ATGTTTTCAA
1 GTGTTTTCAA
17628330 CAATTCCCGT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 30 0.79
37 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (35 bp):
GTGTTTTCAAAAAAATTCATGTTTCAAAAATCTTC
Found at i:17628342 original size:35 final size:34
Alignment explanation
Indices: 17628269--17628369 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 34
17628259 AAAAAATTCA
* ***
17628269 TGTTTCAAAAATCTTCGTGTTTTCAAAAATTTTGG
1 TGTTTC-AAAATTTTCGTGTTTTCAAAAATTCCCG
* *
17628304 TGTTTCTAAAATTTTCATGTTTTCAACAATTCCCG
1 TGTTTC-AAAATTTTCGTGTTTTCAAAAATTCCCG
*
17628339 TGTTTCACAAATTTTTGTGTTTTCAAAAATT
1 TGTTTCA-AAATTTTCGTGTTTTCAAAAATT
17628370 ATTATCGTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 1 0.02
35 54 0.98
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.48
Consensus pattern (34 bp):
TGTTTCAAAATTTTCGTGTTTTCAAAAATTCCCG
Found at i:17636097 original size:3 final size:3
Alignment explanation
Indices: 17636089--17636138 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
17636079 AACCATAGCA
*
17636089 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17636137 AA
1 AA
17636139 CTTTAACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:17638451 original size:44 final size:44
Alignment explanation
Indices: 17638388--17638475 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
17638378 AGACCTGGTC
17638388 AACTTTGAGCAAACCCTCAAAGTTCTCCAAATACCAAAGGCTTA
1 AACTTTGAGCAAACCCTCAAAGTTCTCCAAATACCAAAGGCTTA
17638432 AACTTTGAGCAAACCCTCAAAGTTCTCCAAATACCAAAGGCTTA
1 AACTTTGAGCAAACCCTCAAAGTTCTCCAAATACCAAAGGCTTA
17638476 GGTATTGACC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (44 bp):
AACTTTGAGCAAACCCTCAAAGTTCTCCAAATACCAAAGGCTTA
Found at i:17646023 original size:2 final size:2
Alignment explanation
Indices: 17646016--17646051 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17646006 TATTACAAGT
17646016 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17646052 AAATCCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17647516 original size:8 final size:8
Alignment explanation
Indices: 17647505--17647578 Score: 51
Period size: 8 Copynumber: 8.9 Consensus size: 8
17647495 TAATTAATTT
*
17647505 TTTAAGAA
1 TTTAAAAA
17647513 TTTAAAAA
1 TTTAAAAA
17647521 TTTTAAAAA
1 -TTTAAAAA
*
17647530 TATAAAAA
1 TTTAAAAA
*
17647538 ATT-AAAA
1 TTTAAAAA
*
17647545 TTAAAAATTA
1 TTTAAAA--A
*
17647555 TTTAAATTA
1 TTTAAA-AA
17647564 TTTAAAAA
1 TTTAAAAA
*
17647572 TATAAAA
1 TTTAAAA
17647579 GTTATTTTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
7 5 0.10
8 25 0.49
9 15 0.29
10 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (8 bp):
TTTAAAAA
Found at i:17647526 original size:17 final size:16
Alignment explanation
Indices: 17647504--17647572 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 16
17647494 TTAATTAATT
17647504 TTTTAAGAATTTAAAAA
1 TTTTAA-AATTTAAAAA
*
17647521 TTTTAAAAATATAAAAA
1 TTTT-AAAATTTAAAAA
*
17647538 -ATTAAAA-TTAAAAA
1 TTTTAAAATTTAAAAA
17647552 TTATTTAAATTATTTAAAAA
1 -T-TTTAAA--ATTTAAAAA
17647572 T
1 T
17647573 ATAAAAGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
14 6 0.15
15 4 0.10
16 2 0.05
17 18 0.44
18 2 0.05
19 2 0.05
20 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
TTTTAAAATTTAAAAA
Found at i:17647570 original size:20 final size:20
Alignment explanation
Indices: 17647545--17647614 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
17647535 AAAATTAAAA
17647545 TTAAAAATTATTTAAATTAT
1 TTAAAAATTATTTAAATTAT
*
17647565 TTAAAAA-TA-TAAAAGTTATT
1 TTAAAAATTATTTAAA-TTA-T
* *
17647585 TTTAAAATT-TTTAAAATTAA
1 TTAAAAATTATTT-AAATTAT
17647605 TTAAAAATTA
1 TTAAAAATTA
17647615 ACATTTCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
18 4 0.10
19 5 0.13
20 22 0.56
21 5 0.13
22 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
TTAAAAATTATTTAAATTAT
Found at i:17667373 original size:21 final size:22
Alignment explanation
Indices: 17667349--17667397 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
17667339 TTTGTTATTC
*
17667349 ATTATTTTACTTAATTAA-TTT
1 ATTATTTTACTTAATTAACCTT
** *
17667370 ATTAAATTACTTATTTAACCTT
1 ATTATTTTACTTAATTAACCTT
17667392 ATTATT
1 ATTATT
17667398 AACATATAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTATTTTACTTAATTAACCTT
Found at i:17688260 original size:25 final size:24
Alignment explanation
Indices: 17688207--17688265 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
17688197 ATTTTAAAAT
* *
17688207 AATTATCTAATTTTTCAATTTATTG
1 AATTAT-TAATTTTTCAATTAATTA
17688232 AATTATTAATATTTT-ATATTAATTA
1 AATTATTAAT-TTTTCA-ATTAATTA
*
17688257 AATTTTTAA
1 AATTATTAA
17688266 GAAAATAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (24 bp):
AATTATTAATTTTTCAATTAATTA
Found at i:17701845 original size:32 final size:32
Alignment explanation
Indices: 17701762--17701901 Score: 133
Period size: 32 Copynumber: 4.4 Consensus size: 32
17701752 AATGGCTACT
* * *
17701762 AGCCATAAGTA-CAGTAATATGATTGGTACAA
1 AGCCATCAGTAGCAGTAATATGATCGGCACAA
*
17701793 AGCCAT-AGTAGTAGTAATATGATCGGCACAA
1 AGCCATCAGTAGCAGTAATATGATCGGCACAA
* * * *
17701824 AGCCATCAGTAGCAGTGATATGACCAGCACAC
1 AGCCATCAGTAGCAGTAATATGATCGGCACAA
* * * *
17701856 AG-CTTACAGTAACGGTAATATGATCTGCACAA
1 AGCCAT-CAGTAGCAGTAATATGATCGGCACAA
*
17701888 AACCATCAGTAGCA
1 AGCCATCAGTAGCA
17701902 TCGCAACAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
30 4 0.05
31 31 0.36
32 49 0.57
33 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (32 bp):
AGCCATCAGTAGCAGTAATATGATCGGCACAA
Found at i:17701938 original size:26 final size:26
Alignment explanation
Indices: 17701903--17701953 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
17701893 TCAGTAGCAT
17701903 CGCAACAAAGCTGCCAGCAACAGTAC
1 CGCAACAAAGCTGCCAGCAACAGTAC
* * *
17701929 CGCAGCAAAGCTGCTAGTAACAGTA
1 CGCAACAAAGCTGCCAGCAACAGTA
17701954 TATGTGGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.29, G:0.22, T:0.12
Consensus pattern (26 bp):
CGCAACAAAGCTGCCAGCAACAGTAC
Found at i:17701974 original size:27 final size:26
Alignment explanation
Indices: 17701944--17702006 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
17701934 CAAAGCTGCT
17701944 AGTAACAGTATATGTGGCCA-AGCCACC
1 AGTAACAGTAT-TGTGG-CAGAGCCACC
*
17701971 AGTAACAATGATTGTGGCAGAGCCACC
1 AGTAACAGT-ATTGTGGCAGAGCCACC
17701998 AGT-ACAGTA
1 AGTAACAGTA
17702007 CTTCTTCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
26 6 0.19
27 23 0.72
28 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
AGTAACAGTATTGTGGCAGAGCCACC
Found at i:17702256 original size:26 final size:26
Alignment explanation
Indices: 17702221--17702315 Score: 109
Period size: 27 Copynumber: 3.6 Consensus size: 26
17702211 TAACAAAGGT
*
17702221 ATTACAGTCATTTTACCTATAGGGGC
1 ATTACGGTCATTTTACCTATAGGGGC
* * *
17702247 ATCATGGTCATTTTACCTTATAGAGGC
1 ATTACGGTCATTTTACC-TATAGGGGC
* * *
17702274 ATTACAGTCATTTTACCCTACAGGTGC
1 ATTACGGTCATTTTA-CCTATAGGGGC
17702301 ATTACGGTCATTTTA
1 ATTACGGTCATTTTA
17702316 TAAATATTGG
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
26 14 0.25
27 40 0.71
28 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (26 bp):
ATTACGGTCATTTTACCTATAGGGGC
Found at i:17708664 original size:21 final size:21
Alignment explanation
Indices: 17708638--17708680 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17708628 TATTAACGAG
17708638 TCTATTTTTAATTGAAATAAA
1 TCTATTTTTAATTGAAATAAA
17708659 TCTATTTTTAATTGAAATAAA
1 TCTATTTTTAATTGAAATAAA
17708680 T
1 T
17708681 GGTAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (21 bp):
TCTATTTTTAATTGAAATAAA
Found at i:17730932 original size:26 final size:26
Alignment explanation
Indices: 17730884--17730933 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
17730874 TGAATAATCA
*
17730884 CTCTCATTATTGCCATTACATTTCTG
1 CTCTCATTATTGCCATAACATTTCTG
*
17730910 CTCTCACTT-TTGCCATAATATTTC
1 CTCTCA-TTATTGCCATAACATTTC
17730934 CAATTATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.20, C:0.28, G:0.06, T:0.46
Consensus pattern (26 bp):
CTCTCATTATTGCCATAACATTTCTG
Found at i:17738609 original size:20 final size:20
Alignment explanation
Indices: 17738586--17738626 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
17738576 TTTGGAGAAA
*
17738586 AGAAAGAATGATGAATGATT
1 AGAAAGAATGAGGAATGATT
17738606 AGAAAGAATGAGGAATGATT
1 AGAAAGAATGAGGAATGATT
17738626 A
1 A
17738627 AGGGATGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (20 bp):
AGAAAGAATGAGGAATGATT
Found at i:17744534 original size:17 final size:17
Alignment explanation
Indices: 17744512--17744546 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
17744502 TGCTTCTTTA
17744512 ACTCTTCAAAAGCTTCC
1 ACTCTTCAAAAGCTTCC
17744529 ACTCTTCAAAAGCTTCC
1 ACTCTTCAAAAGCTTCC
17744546 A
1 A
17744547 AACATGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.34, G:0.06, T:0.29
Consensus pattern (17 bp):
ACTCTTCAAAAGCTTCC
Found at i:17747921 original size:30 final size:30
Alignment explanation
Indices: 17747887--17747944 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17747877 GTACCACTAA
*
17747887 ATTGGCCCACCGTTTGTAGTATTTGAAAAG
1 ATTGGCCCACAGTTTGTAGTATTTGAAAAG
* *
17747917 ATTGGTCCAGAGTTTGTAGTATTTGAAA
1 ATTGGCCCACAGTTTGTAGTATTTGAAA
17747945 CATCACGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (30 bp):
ATTGGCCCACAGTTTGTAGTATTTGAAAAG
Found at i:17764548 original size:27 final size:27
Alignment explanation
Indices: 17764503--17764811 Score: 309
Period size: 27 Copynumber: 11.3 Consensus size: 27
17764493 TATAATAGTT
*
17764503 ATTTTACCCTA-GGAGGGTATTTTGGTC
1 ATTTTACCCTACGG-GGGTATTTCGGTC
* *
17764530 ATTTTACCCTACGGTGGTATTTCAGTC
1 ATTTTACCCTACGGGGGTATTTCGGTC
*
17764557 ATTTTATCCTACAGGGAGGGGGTATTTCGGTC
1 ATTTTACCCTAC-----GGGGGTATTTCGGTC
* *
17764589 ATTTTACCCTACAGTGGTATTTCGGTC
1 ATTTTACCCTACGGGGGTATTTCGGTC
*
17764616 ATTTTACACTACGGGGGTATTTCGGTC
1 ATTTTACCCTACGGGGGTATTTCGGTC
* *
17764643 ATTTTACCCTACGAGGGTATTTCAGTC
1 ATTTTACCCTACGGGGGTATTTCGGTC
*
17764670 ATTTTACCCTACGGGGGTATTTTGGTC
1 ATTTTACCCTACGGGGGTATTTCGGTC
*** **
17764697 ATTTTACCCTATAAGGGTATTTTAGTC
1 ATTTTACCCTACGGGGGTATTTCGGTC
**
17764724 ATTTTACCCTA-GAGGGGTATTTCAATC
1 ATTTTACCCTACG-GGGGTATTTCGGTC
* *** * *
17764751 ATTTAACCCTA-TAAGGTATTTCAGTT
1 ATTTTACCCTACGGGGGTATTTCGGTC
*
17764777 ATTTTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTACGGGGGTATTTCGGTC
*
17764804 ATTCTACC
1 ATTTTACC
17764812 TATTTGGGGG
Statistics
Matches: 235, Mismatches: 39, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
26 20 0.09
27 189 0.80
28 2 0.01
32 24 0.10
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (27 bp):
ATTTTACCCTACGGGGGTATTTCGGTC
Found at i:17764561 original size:54 final size:53
Alignment explanation
Indices: 17764503--17764811 Score: 361
Period size: 54 Copynumber: 5.7 Consensus size: 53
17764493 TATAATAGTT
* *
17764503 ATTTTACCCTA-GGAGGGTATTTTGGTCATTTTACCCTACGGTGGTATTTCAGTC
1 ATTTTACCCTACGG-GGGTATTTCGGTCATTTTACCCTACAG-GGTATTTCAGTC
* *
17764557 ATTTTATCCTACAGGGAGGGGGTATTTCGGTCATTTTACCCTACAGTGGTATTTCGGTC
1 ATTTTACCCTAC-----GGGGGTATTTCGGTCATTTTACCCTACAG-GGTATTTCAGTC
*
17764616 ATTTTACACTACGGGGGTATTTCGGTCATTTTACCCTACGAGGGTATTTCAGTC
1 ATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCTAC-AGGGTATTTCAGTC
* * *
17764670 ATTTTACCCTACGGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTTTAGTC
1 ATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCTA-CAGGGTATTTCAGTC
** * * * *
17764724 ATTTTACCCTA-GAGGGGTATTTCAATCATTTAACCCTATAAGGTATTTCAGTT
1 ATTTTACCCTACG-GGGGTATTTCGGTCATTTTACCCTACAGGGTATTTCAGTC
* *
17764777 ATTTTACCCTATGGGGGTATTTCGGTCATTCTACC
1 ATTTTACCCTACGGGGGTATTTCGGTCATTTTACC
17764812 TATTTGGGGG
Statistics
Matches: 222, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
53 41 0.18
54 130 0.59
55 2 0.01
59 47 0.21
60 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (53 bp):
ATTTTACCCTACGGGGGTATTTCGGTCATTTTACCCTACAGGGTATTTCAGTC
Found at i:17767956 original size:27 final size:27
Alignment explanation
Indices: 17767918--17768768 Score: 717
Period size: 27 Copynumber: 31.3 Consensus size: 27
17767908 AATCAGCGTC
*
17767918 TAAAATGACTGAAATAGCCTCGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* *
17767945 TAAAATGACTGAAATACCTTCGATGGC
1 TAAAATGACTGAAATACCCTCGATGGG
17767972 TAAAAAT-ACTGAAATACCCTCGATGGG
1 T-AAAATGACTGAAATACCCTCGATGGG
17767999 TAAAATGACTGAAATACCCTCGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* *
17768026 TAAAATTA-TCGAAATACCTTCGATGGG
1 TAAAATGACT-GAAATACCCTCGATGGG
* * *
17768053 TAAAATTACCGAAATACCCCCGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* * *
17768080 TAAAATTACCGAAATACCATCGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* * *
17768107 TAATATTAC-GAAATA-CCTTGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
*
17768132 T-AAATTA-TCGAAATACCCTCGATGGG
1 TAAAATGACT-GAAATACCCTCGATGGG
* *
17768158 TAAATTGACCGAAATACCCTCGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* * *
17768185 TAACATGACTAAAATACCCCCGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
*
17768212 TAAAATTA-TCGAAATACCCTCGATGGG
1 TAAAATGACT-GAAATACCCTCGATGGG
* *
17768239 TTAAATTACTGAAATACCCTCGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* **
17768266 TAAAATTACCAAAATA-CCTCTGATGGG
1 TAAAATGACTGAAATACCCTC-GATGGG
* * * ***
17768293 TAAAATAACTAAAATACCCTCAACATG
1 TAAAATGACTGAAATACCCTCGATGGG
**
17768320 TAAAATGACCAAAATACCCTCGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* *
17768347 TAAAATGACTGAAATAGCCTCGTTGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* * *
17768374 TAAAGTGACTAAAATTATCGAAATACCCTCAATGAG
1 TAAAATGAC--------T-GAAATACCCTCGATGGG
* **
17768410 TAAAATGACCGAAATACCCTCGATGTT
1 TAAAATGACTGAAATACCCTCGATGGG
17768437 TAAAATGA-TCGAAATACCCTCGATGGG
1 TAAAATGACT-GAAATACCCTCGATGGG
* **
17768464 TAAAATGATTGAAATACCCTTAATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* *
17768491 TAAAATTA-TCGAAATACCCTCAATGGG
1 TAAAATGACT-GAAATACCCTCGATGGG
* * * * *
17768518 TAAAATTA-TCAAAATATCGTCGAAGGG
1 TAAAATGACT-GAAATACCCTCGATGGG
* *
17768545 TAAAATTGTC-AAAATACCCTCGATGGG
1 TAAAA-TGACTGAAATACCCTCGATGGG
* ** *
17768572 TAAAATTACAAAAATACCCTTGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* * **
17768599 TAAAATTA-TCGAAA-ACCCCCGAACGG
1 TAAAATGACT-GAAATACCCTCGATGGG
* *
17768625 TAAAATTAAC-GAAATACCCTCAATGGG
1 TAAAA-TGACTGAAATACCCTCGATGGG
* * *
17768652 TAAAATTACAGAAATACCCTTGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* * *
17768679 TAAAATGACTAAAATACCCCCGAAGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* * *
17768706 TAAAATGGCCGAAATACCCTTGATGGG
1 TAAAATGACTGAAATACCCTCGATGGG
* * *
17768733 TAAAATTACCGAAATACCCT-TATAGGG
1 TAAAATGACTGAAATACCCTCGAT-GGG
17768760 TAAAATGAC
1 TAAAATGAC
17768769 CGTATACCCC
Statistics
Matches: 681, Mismatches: 109, Indels: 68
0.79 0.13 0.08
Matches are distributed among these distances:
24 5 0.01
25 15 0.02
26 52 0.08
27 575 0.84
28 12 0.02
35 1 0.00
36 21 0.03
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCTCGATGGG
Found at i:17768451 original size:90 final size:90
Alignment explanation
Indices: 17768304--17768467 Score: 242
Period size: 90 Copynumber: 1.8 Consensus size: 90
17768294 AAAATAACTA
*
17768304 AAATACCCTCAACATGTAAAATGACCAAAATACCCTCGATGGGTAAAATGACTGAAATAGCCTCG
1 AAATACCCTCAACATGTAAAATGACCAAAATACCCTCGATGGGTAAAATGACTGAAATACCCTCG
*
17768369 TTGGGTAAAGTGACTAAAATTATCG
66 ATGGGTAAAGTGACTAAAATTATCG
* * **
17768394 AAATACCCTCAATGA-GTAAAATGACCGAAATACCCTCGATGTTTAAAATGA-TCGAAATACCCT
1 AAATACCCTCAA-CATGTAAAATGACCAAAATACCCTCGATGGGTAAAATGACT-GAAATACCCT
17768457 CGATGGGTAAA
64 CGATGGGTAAA
17768468 ATGATTGAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
89 1 0.02
90 64 0.97
91 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (90 bp):
AAATACCCTCAACATGTAAAATGACCAAAATACCCTCGATGGGTAAAATGACTGAAATACCCTCG
ATGGGTAAAGTGACTAAAATTATCG
Found at i:17768998 original size:26 final size:26
Alignment explanation
Indices: 17768960--17769057 Score: 115
Period size: 26 Copynumber: 3.8 Consensus size: 26
17768950 TTGCCACAAA
* *
17768960 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGTTAGTGGCAGCTTTGCTGCAT
* * *
17768986 TACTGATAGTGGCAGCTCTGCTGCCT
1 TACTGTTAGTGGCAGCTTTGCTGCAT
*
17769012 TACTGTTAGTGGCAACTTTGCTGCAT
1 TACTGTTAGTGGCAGCTTTGCTGCAT
* * *
17769038 TACTATTATTGCCAGCTTTG
1 TACTGTTAGTGGCAGCTTTG
17769058 TTGCGATATT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
TACTGTTAGTGGCAGCTTTGCTGCAT
Done.